With words of comfort and resolve, President Bush joined the nation in remembering "a year of sorrow, of empty places" since the attacks that drew America into war.
He cautioned Americans that the United States has "determined enemies" and is "not invulnerable to their attacks."
"For all Americans, it has been a year of adjustment, of coming to terms with the difficult knowledge that our nation has determined enemies and that we are not invulnerable to their attacks," he said.
Bush also reminded Americans what is at stake in the war on terrorism.
"The attack on our nation was also an attack on the ideals that make us a nation. Our deepest national conviction is that every life is precious, because every life is the gift of a creator who intended us to live in liberty and equality."
Earlier, as daylight began to ebb, President Bush laid a wreath at Manhattan's Ground Zero in one of several daylong series of events to commemorate the anniversary of the attacks.
Mr. Bush embraced fathers and sons, kissed mothers and daughters and wives of the more than 2,800 people killed there last Sept. 11 after hijacked airliners sliced through New York's World Trade Center.
In New York, Washington and Pennsylvania – the epicenters of last year's terror attacks – and in countless cities and towns around the country, Americans paused Wednesday to remember the thousands who were killed on Sept. 11, 2001.
New York City's official memorial service got under way with a moment of silence at 8:46 a.m., the exact time the first hijacked jet crashed into the World Trade Center.
"Again today we are a nation that mourns. Again today we take into our hearts and minds those who perished on this site one year ago," said Mayor Michael Bloomberg.
Former New York Mayor Rudolph Giuliani led a parade of dignitaries reading the names of the 2,801 people killed or missing in the trade center attack. Name readers included relatives of victims from hard-hit companies like Cantor Fitzgerald and Aon. Secretary of State Colin Powell, Sen. Hillary Rodham Clinton and actor Robert De Niro also were on the list.
The first name read was that of Gordon Aamoth Jr., 32, who worked for investment firm Sandler O'Neill & Partners on the south tower's 104th floor. The roll ended with Igor Zukelman, 29, who worked at Fiduciary Trust Company International in the north tower.
"They were our neighbors, our husbands, our children, our sisters, our brothers and our wives. They were our countrymen and our friends. They were us," Bloomberg said.
At 10:28 a.m., the time the second tower collapsed, a second moment of silence was observed.
On the eve of the anniversary, the Bush administration raised the nationwide terror alert to its second-highest level, heightened security at federal buildings and landmarks, and closed nine U.S. embassies overseas as new intelligence warned of car bombings, suicide attacks and other strikes.
Pentagon officials said Wednesday that the U.S. military command in charge of the region from East Africa through the Arabian Peninsula to Pakistan had raised its security level.
At home, the U.S. military expanded jet fighter patrols over some 10 cities and armed missile launchers that had already been stationed near several Washington sites, defense officials said.
Despite the threats, federal officials told Americans to go ahead with their plans to commemorate Sept. 11 at gatherings and not change their work, school or travel schedules.
Mr. Bush's emotional return to New York was his final stop in a daylong tour of the three sites scarred by terrorism — a rebuilt and now unblemished Pentagon, a field of golden grass in Pennsylvania and the dusty pit where the twin towers once soared.
At the Pentagon, where 189 people were killed on Sept. 11 when American Flight 77 crashed into the building, the president and Defense Secretary Donald Rumsfeld stood beneath a massive American flag as it was unfurled on the side of the restored building.
"The murder of innocents cannot be explained, only endured," a somber president said. "Though they died in tragedy, they did not die in vain," Mr. Bush told a crowd of several thousand.
The ceremony was moving and the rebuilt Pentagon is impressive, but, as CBS News Correspondent David Martin reports,the reality of a nation on edge is grim as anti-aircraft radars and missile batteries remained stationed around Washington and police boats patrolled the Potomac River.
The president then traveled to Shanksville, Pa., to take part in another solemn ceremony in honor of the passengers and crew of United Flight 93, who have been hailed as heroes for struggling to take back their hijacked plane from four terrorists.
A bell tolled for each of the 40 victims, accompanied by the reading of each of their names, leading up to the moment that the plane crashed at 10:06 a.m. last Sept. 11.
In their shared sorrow, relatives of those lost aboard Flight 93 turned again to that moment of mid-air heroics, and, as CBS News Correspondent Mark Strassman reports, found their own strength in numbers.
The day was being marked in smaller ways in thousands of American cities and towns that felt the shockwaves of the worst terrorist attacks in U.S. history.
The strains of Mozart's Requiem were heard in every time zone, sung by symphonies and school choirs.
Splinters of the destroyed buildings were on display in states such as Nevada, Tennessee, Ohio and Wyoming.
Public schools in several states honored the day with special events, including a moment of silence at 9:40 a.m. in all Washington, D.C. classrooms. That's the moment when a plane carrying three Washington students and three teachers hit the Pentagon.
On the sprawling statehouse lawn in Columbus, Ohio, 2,999 American flags and one Ohio flag were arranged to depict the twin towers. In San Francisco's Washington Square, more than 3,000 flags flew, including those of 14 other countries whose citizens were among the victims.
At Boston's Logan International Airport, where the two planes that struck the trade center took off, all ground operations stopped at 8:46 a.m.
Attesting to the global impact of Sept. 11, gatherings to mark the anniversary were also taking place around the world. Nearly 500 foreigners from 91 countries lost their lives in the terror attacks.
In Britain, which lost 67 citizens, more than any country other than the United States, a service of remembrance and commemoration was held at London's St. Paul's Cathedral.
In Japan, which lost 24 citizens, flowers were left in front of the U.S. embassy, and a group of Buddhist monks gathered in the same place, to chant memorial prayers.
At the Vatican, Pope John Paul II said Wednesday that nothing can justify "such an aberration" as the Sept. 11 attacks, and urged rich countries to do all they can to put an end to "scandalous" injustices.
"Terrorism is and always will be a show of inhuman ferocity," the pope told some 8,000 pilgrims packing a Vatican auditorium. "It will never be able to solve conflicts among human beings."
Other memorials were taking place in Australia, New Zealand, Israel, Germany, Denmark, Finland and France, where President Jacques Chirac told a ceremony at the heavily guarded U.S. Embassy in Paris that "France knows what it owes America."