The weeklong visit culminated in a 20-nation meeting at a military airbase outside Rome on Tuesday and a meeting with Pope John Paul at the Vatican in the afternoon.
The president left Rome for Washington later Tuesday afternoon.
During the week, Mr. Bush visited Germany, France, Italy and Russia, where he signed a landmark pact with Russian President Vladimir Putin to slash their countries' deployed nuclear warheads.
In Rome, NATO and Russian leaders put their Cold War enmity behind them and crowned the transformation in their relations since Sept. 11 with a new council for cooperation on tasks ranging from terrorism to arms control.
"Two former foes are now joined as partners, overcoming 50 years of division and a decade of uncertainty," Mr. Bush said as Russia prepared to take its place at the NATO table.
"The significance of this meeting is difficult to overestimate," said Putin, noting that such a role for Russia would have been unthinkable just a few years ago. "We have come a long way from confrontation to dialogue, and from confrontation to cooperation."
Putin noted that Russia is not being admitted as a full partner and its NATO involvement will be limited to certain areas. They include crisis management, peacekeeping and such military areas as air defense, search-and-rescue operations and joint exercises.
"We must understand this Rome Declaration ... is only a beginning," said Putin.
But what is being hailed as the last nail in the coffin of the Cold War could be the first nail in the coffin of NATO, reports CBS News Chief White House Correspondent John Roberts. With the Soviet threat now gone, the alliance is struggling to remain relevant.
Mr. Bush wants to reshape NATO as a counter-terrorism force able to project power to all corners of the globe, and he is leaning on Europe to transform its bulky Cold War defenses into a lighter, faster, more mobile military.
"All militaries ought to be modernized, all militaries need to be modernized to meet the true threats of the 21st century," Mr. Bush said.
But allies balk at both spending the money and committing troops to conflicts outside Europe.
And with five to seven militarily poor nations from former Eastern Europe set to soon join the alliance next – a move Russia opposes – critics believe NATO could become just another international soapbox and a drag on Mr. Bush's goals in the war on terror.
Later Tuesday, Mr. Bush paid a visit to Pope John Paul II at the Vatican - the last stop on his European trip. A White House spokesman said that Mr. Bush raised the issue of the Catholic Church sexual abuse scandal. The two men also reportedly discussed the Middle East and Russia.
The NATO meeting was the second get-together in a week for Presidents Putin and Bush. Mr. Bush spent three days in Russia last week, visiting both Moscow and St. Petersburg. In Moscow, the two leaders agreed to slash their strategic nuclear arsenals to one-third of the present levels over the next decade.
On Monday, Mr. Bush was in France, where he marked the Memorial Day holiday with a tour of Normandy, site of the June 6, 1944, D-Day invasion that ultimately liberated France and turned the tide of World War II.