Vanderlei de Lima of Brazil was pushed off the road by a lone spectator while leading the men's Olympic marathon on Sunday, the final event of the 16-day Games.
The man was arrested and taken to a police station. There were no details of his name or nationality.
After being pushed into the crowd, De Lima got away from the protestor and rejoined the race, holding his leg, with around 15 minutes to run.
He soon lost the lead to Italian Stefano Baldini. Baldini won the race and De Lima took bronze.
"The man has been arrested and is now being taken to the police station," a police spokeswoman said. "More information will be available later."
The spectator, dressed in a kilt with some writing on his back, resembled the Irishman who interrupted the British Formula One Grand Prix at Silverstone last year.
Cornelius Horan ran on to the main Hangar Straight in that race as cars approached at speeds in excess of 240kph. He was sentenced to two months imprisonment for his action.
At the Munich Olympics in 1972 a hoaxster snuck on to the track a couple of minutes before the leading runner reached the stadium and ran a full lap, pretending to be a competitor, before being dragged away by security guards.
Four years ago, a well-known Australian prankster broke through security at the Sydney Marathon. He failed to disrupt the race and was soon carted off by police.