As a stoic Yeltsin looked on, the coffins of Czar Nicholas II, his family, and servants were lowered into a large crypt beneath the floor of the gilded, 18th-century St. Peter and Paul Cathedral.
CBS News Senior European Correspondent Tom Fenton reports that the burial of Nicholas II in his former imperial capital is something no one could have dreamed of.
It was exactly 80 years to the day since Nicholas II and the rest of his family were brutally executed and buried in a common grave. Nicholas was the last of the Romanov emperors who ruled Russia for three centuries. After abdicating in 1917 in the throes of the Russian Revolution, he was murdered on July 17, 1918, along with his wife, their five children, and four servants.
Now, they are now being given a Christian burial.
The Russian Orthodox ceremony took place in the presence of dozens of relatives of Nicholas II, diplomats from 50 countries, and Prince Michael of Kent, a member of the British royal family, which is related to Russian royalty. They all stood and held lit candles at the cathedral on the banks of the Neva River.
"We must tell the truth: The [czar's] massacre has become one of the most shameful pages of our history," Yeltsin told the dignitaries in the cathedral and a nationwide television audience. "By burying the remains of the innocent victims, we want to expiate the sins of our ancestors."
The czar's family members tossed white sand, representing the Earth, onto the coffins before the crypt was covered. On the river bank, cannons boomed in a 19-shot salute - two shy of the customary 21 because the czar had abdicated.
With a dozen bearded priests in gold-and-white robes officiating, the ceremony was handled with an understated dignity, a sharp contrast to the months of controversy that preceded the event.
Many leading Russian figures, including the head of the Russian Orthodox Church, skipped the service because of the disputes. Yeltsin was planning to stay away as well, but changed his mind and announced Thursday he would participate.
In fact, the ceremony was technically not a state funeral because th Greek and the Russian Orthodox Church says it does not believe these are actually the remains of Nicholas II - or, at least, it is not 100 percent sure.
DNA and other forsensic tests in the United States, Russia, and Britain have provided overwhelming evidence of the identification of the remains.
Fenton reports the priests were there blessing the remains, and Yeltsin was there, in his words, to tell the truth that has been concealed for the past 80 years.
Many Russians hope that by burying the czar alongside his ancestors they will also bury some of the bitterness of the 20th century Russian history.
It has been difficult to turn on a television in Russia this week without seeing programs about the royal family, with archival footage of Nicholas, his wife, Alexandra, and their children. Russians who grew up in the communist era knowing little about the Romanovs are being inundated with their history.
About 1,500 people gathered outside the fortress Friday morning, though they were not able to see the ceremonies. A few dozen were there to protest the burial.
"Factories are closed. People aren't getting their pay. What's going on with this funeral?" said Vyacheslav Marichev, a former politician.
After the collapse of the Soviet Union, nine of the 11 bodies were recovered from a desolate forest outside the Ural Mountains city of Yekaterinburg. That is where the burial ceremonies began Wednesday, when the bones were taken from the city's police morgue and placed in small, skeleton-sized coffins.
The coffins were flown to St. Petersburg on Thursday, and thousands of Russians stood in silence along the city's streets and river embankments Thursday as the czar's cortege passed by.
The only question that remains now, Fenton says, is, when will Lenin be buried? The Communist leader's body has lain embalmed all these years in Red Square, and it's known that Yeltsin would like to lay him to rest as well.