In the women's race, defending champion Catherine Ndereba of Kenya became the first four-time winner of the marathon, coming from behind to overtake Ethiopia's Elfenesh Alemu.
Negussie, fifth last year, finished the 109th edition of the Boston marathon in an official time of 2 hours 11 minutes 45 seconds. The course record of 2:07:15 was set by Cosmas Ndeti of Kenya in 1994.
Wilson Onsare of Kenya finished second on 2:12:21 and fellow Kenyan Benson Cherono came in third at 2:12:48.
Kenyan men had won 13 of the previous 14 Boston marathons and runners from Kenya claimed five of the top seven spots this year.
Negussie, who became the first Ethiopian winner since Abebe Mekonnen in 1989, put distance between himself and a pack of Kenyan runners, including champion Timothy Cherigat, after Heartbreak Hill, the steepest climb of the course.
The 25-year-old said he broke from the pack because he was concerned one of Kenyan runners might speed ahead like last year.
"I made the move because I knew there were a lot of Kenyans. My second move made a difference for me to win the marathon," Negussie said through a translator at a news conference.
AGONISING ASCENT
Ndereba, who won in 2000, 2001 and 2004, also made her break on Heartbreak Hill, an agonising 600-metre ascent shortly after the 20-mile mark, passing Alemu enroute to an official time of 2:25:13.
Ndereba and Alemu also finished first and second in last year's race.
Alemu, who was more than one minute ahead of Ndereba at the halfway point, finished with a time of 2:27:03. Bruna Genovese of Italy came in third at 2:29:51.
Ndereba said she fell behind early because her legs felt heavy but as the race continued she felt more relaxed.
"As I kept on pushing the pace, I could feel my body moving and I thought. 'Wow, I can do it,'" Ndereba said.
The runners said the heat played a factor in keeping times slow, even though it was much cooler than last year.
America's Alan Culpepper finished fourth, the highest U.S. male finisher since 1987.
Last year's winner and early front-runner Cherigat faltered down the stretch and finished sixth.e
