Ekimov, one of the early starters, posted a time of 57 minutes and 40 seconds, which could not be overhauled by the bigger names who started behind him.
Road race gold medallist Jan Ullrich, the World Time Trial Champion, was eight seconds adrift and took silver, while Tour de France winer Lance Armstrong bagged bronze, 34 seconds behind the winner.
British medal hopes Chris Boardman, who had voiced criticism of the course prior to the race, and David Millar failed to make an impression.
Struggle
Boardman had to struggle to finish 11th, one minute and 52 seconds behind Ekimov while Millar trailed in 16th, more than two and a half minutes off the pace.
Ekimov's victory gave Russia their first cycling gold since he was in the title-winning foursome in the track team pursuit in 1988 at Seoul.
Ekimov, 34, is the first Russian to win an Olympic road gold since 1980 when Sergei Soukhoroutchenkov took the road race and the Soviet Union triumphed in the road team time trial, which was replaced in Atlanta by the individual time trial.
After the race Boardman said: "It's a good job I'm retiring in four weeks' time."
Boardman, 32, who will retire from competition after the world championships and a new attempt on the world hour record on 27 October, revealed earlier this week he has been suffering from the bone-wasting disease osteopenia for the past two years.
And after scaling the heights earlier in his career, he admitted his performance here had confirmed what he has known for some time about the debilitating effects of the disease on his cycling.
"It's getting harder and harder to perform at this level and I seem to be more and more fragile," he said.
Philosophical
"It has been a bit of a do or die effort in the last few weeks to do the volume of training to create the form to be competitive, and my body is just not recovering from it."
Millar was equally philosophical.
"I am not on top form but at least I finished it - I survived," he said.
"After the first lap I was thinking 'another two laps to go - that's a bit long.'"