Italy's Stefano Baldini took gold in the men's marathon, but his victory was overshadowed after one of the runners was attacked by a protester.
Brazilian Vanderlei de Lima was leading when the man pushed him to the side of the road four miles from the finish.
Soon afterwards, Baldini overtook De Lima to win in a time of two hours 10:54 secs.
Mebrahtom Keflezighi of the United States took silver, while De Lima finished with bronze.
Great Britain's Jon Brown suffered further Olympic misery when he repeated his fourth place in Sydney four years earlier after clocking a time of two hours 12:26 secs.
The protester, wearing a kilt and a green beret and a white placard with the words "The Grand Prix priest. Israel fulfillment of prophecy says the bible, the second coming is near," on it, was immediately arrested and taken to a police station.
Police later revealed it was Cornelius "Neil" Horan, a former priest who disrupted last year's British Grand Prix. He was previously jailed for two months following his race track protest at Silverstone.
A police source said: "The man says he is Irish, he is also drunk. He had been to
a taverna earlier. Police are going through his stuff."
After the incident, De Lima said he was "happy" to win the bronze medal, adding he "maybe would have won" had it not been for the protester.
But after the medal presentation, De Lima said: "If it were not for that lunatic, I am sure I would have won the gold.
"For the way I was running, I was unstoppable.
"I had some troubles in the first kilometres, but I was in a great shape and I am sure I would have won it.
"The attack really surprised me, because I did not think I was his target.
"He did not injure me, but he broke my rhythm and I lost concentration.
"I didn't know if he had a weapon or what his intention was."
A slow pace was set in the early stages in the hot temperatures before Hendrick Ramaala decided to break clear at the 10-mile mark.
But it proved too early for the South African who dropped well behind as the field caught him and then de Lima went alone after 13 miles.
He stayed comfortably in front until the 22-mile mark when he was bundled into the barriers by the protestor.
Even before then he looked likely to be caught by the fast-chasing Baldini but the incident massively helped the Italian's gold chase.
The protester is led away by security guards
Once in front, Baldini looked in little danger of being caught despite the best efforts of
Keflezighi, who had to make do with second.
Remarkably, de Lima managed to hold onto his bronze medal position much to the delight of the crowd, who had watched the earlier incident on the big screen and greeted his entry to the Panathinaiko Stadium with a massive cheer.
After the race, the International Olympic Committee said it was saddened by the incident and awarded de Lima the Pierre de Coubertin Medal at the closing ceremony.
An IOC spokesman said: "We decided to do this in recognition of de Lima's exceptional demonstration of fair play and Olympic values during this evening's marathon."
The IAAF also confirmed that the overall marathon result would not be changed despite the incident.