The 26-year-old Negesse took the tape in 2 hours, 6 minutes flat ahead of Kiprotich (2:06:33) and defending champion and race record-holder Dickson Chumba of Kenya, who came in third (2:06:34).
Negesse’s compatriot Birhane Dibaba won the women’s competition in 2:23:15, capping the first men-women sweep by any nation in race history.
Masato Imai was Japan’s highest men’s finisher at seventh (2:07:39) in a strong field including Kiprotich and five runners who have cracked the 2:05 barrier.
“I think it was a good race but a bit windy,” Negesse said. “I had hoped for a faster time but wasn’t possible given the conditions.
“There were many good runners in the field with fast times from big meets like the Olympics and the world championships. But I didn’t lose any sleep over it.
“I knew if I put in the work and ran the race I’m capable of running, I was good enough to win it.”
Negesse failed to match Chumba’s record from last year by 18 seconds, but his time was still his second best after a 2:04:52 at the Dubai Marathon in January 2013.
But after Dubai, Negesse, who dropped out of school in 2012 to run professionally, injured his left leg and didn’t enter another marathon until Dusseldorf in April last year.
Now that he’s won his second marathon, Negesse’s goal is to challenge the world record of 2:02:57 held by Kenya’s Dennis Kimetto.
“That is a dream of mine,” Negesse said, referring to the only sub-2:03 time in history. “I’m not saying I will do it in my next race, but it is a big goal of mine to eventually do it.
“I spent almost four months getting ready for this race. I won today because I trained hard and worked to overcome an injury that kept me out a while.
“I’m very happy to have won this race because to win a majors race, you need a combination of talent, strength and the will to work hard.”
Chumba was in the lead as late as the 38-km mark, but faded after feeling pain in his stomach. By 40 km, Negesse had seven seconds on Chumba and coasted the rest of the way.
For the Japanese athletes, the race doubled as a qualifier for this summer’s world championships in Beijing.
Former ekiden star Imai put himself in a strong position to make Japan’s team by posting the sixth-fastest time ever by a male Japanese runner and taking nearly three minutes off his previous personal best.
“I was aiming for 2:06, 2:07 at worst,” Imai said. “I just managed to hang on to the end. Up until now, I was getting uptight and winding myself into a knot even before the race started.”