Cruising alone through the final 11 kilometers (seven miles) of the 42.2-kilometer (26.2-mile) race, the 27-year-old Kenyan beat countryman Christopher Cheboiboch by nearly two minutes. Cheboiboch, the 2005 winner here, finished in 2:10:58. Sylvester Chebii was third in 2:12:00 as Kenyans swept the top nine places.
Yego's effort wasn't enough to break the course record. While his time was third-fastest in the race's 10-year history, it was well short of Philip Tarus' record 2:08:33 set in 1999.
"He gave it a hell of a shot for the course record," said race founder Tim Murphy of Elite Racing.
Hellen Kimutai of Kenya won the women's race in 2:32:40. She finished 10 seconds ahead of Svetlana Pretot of France.
It was Yego's first win in a major marathon. He was fourth in the New York City Marathon in November in 2:10:34.
"I did not intend to push it, but the moment I pulled out, there was nobody, so I decided to go," said Yego, who made his move as the course wound through Mission Bay.
Yego felt he might have broken the record if someone had pushed him through the final seven miles to the finish on the parade deck at the Marine Corps Recruit Depot.
Cheboiboch tried but couldn't catch his countryman.
"The guy was a little bit stronger," said Cheboiboch, who won here two years ago in 2:09:17, which until Sunday had been the third-fastest time in the Rock 'n' Roll Marathon's history. "I tried to attack him, but unfortunately, I could not attack him."
Yego and Cheboiboch felt the pacesetters went out too quickly.
The rabbits took the lead pack through the first half of the race in 1:03:41. Cheboiboch thought it should have been 1:04:40 so the runners would have a little left for the finish.
"The rabbit was running too fast and destroyed the whole thing," Cheboiboch said. "If the rabbit ran really smart, this guy would have broken the record. All in all, that was the race, and I'm happy I'm No. 2."
The Rock 'n' Roll Marathon features Elvis impersonators and bands playing at approximately every 1 1/2 kilometers and near the finish line.