Mutai's time of two hours four minutes 15 seconds on the fastest of the big city courses was more than half a minute slower than the world record set by compatriot Patrick Makau in the German capital last year.
His victory gave him an unassailable lead in the world marathon majors series which awards points during a two-year cycle from finish positions in the Boston, London, Berlin, Chicago and New York marathons with a million dollar jackpot split between the men's and women's winners.
"I had the chance to break the world record but after 35 kms I had stomach cramps and I decided to maintain the pace," Mutai told reporters. "I thank God for winning this race and it was possible to break the world record but I tried even though I could not move."
Kenya swept the podium spots with another marathon debutant, 19-year-old Geoffrey Kipsang, finishing in third place a minute and 57 seconds behind the winner.
In the women's race, Ethiopia clinched a one-two double with pre-race favourite Kebede winning he second Berlin marathon in 2:20:30. Her training partner Tirfi Tsegaye was second with Ukraine's Olena Shurhno third.
On a warm and sunny autumn morning more than a million fans lined the streets of Berlin to see race favourite Mutai make a bid for the world record after his failure to make the London Olympics.
Mutai, 30, bettered the world mark in winning the Boston marathon last year but his time of two hours three minutes and two seconds was not recognised because the course does not meet the criteria required for world records.
On Sunday, Mutai pulled away with a group of five runners from the start including a stubborn Kimetto, running his first competitive marathon.
The duo were joined from the start by Kipsang, also making his marathon debut, and Jonathan Mayo, whose personal best of 2:04:56 set in Dubai put him firmly among the pre-race favourites.
The group's time, after a surprisingly bad run between kilometres five and 10, hinted at the 30 kms mark that the world record was slowly slipping away with their time half a minute off Makau's 2011 pace.
Mutai upped the tempo shortly after, pulling away from the rest but with Kimetto, who was looking for a Berlin treble after winning the half-marathon and 25 kms races here, hanging on.
Kimetto remained a menacing presence after he survived another Mutai attempt to shake him off at the 40 kms mark.
"I was not expecting to finish close to him since I knew I could not beat him," said Kimetto. "But I am happy with my run and in future, I will try for the world record."
Going into the final stretch and through the Brandenburg Gate, Kimetto, who clocked the fastest marathon debut ever, had no reserves to launch a final challenge with Mutai clinging on for victory.
1. Geoffrey Mutai (Kenya) 2:04:15
2. Dennis Kimetto (Kenya) 2:04:16
3. Geoffrey Kipsang (Kenya) 2:06:12
4. Nicholas Manza (Kenya) 2:08:28
5. Josphate Keiyo (Kenya) 2:08:41
6. Jonathan Kiplimo Maiyo (Kenya) 2:09:19
7. Eliud Kiptanui (Kenya) 2:09:59
8. Felix Keny (Kenya) 2:10:22
9. Masakazu Fujiwara (Japan) 2:11:31
10. Suehiro Ishikawa (Japan) 2:11:46
1. Aberu Kebede (Ethiopia) 2:20:30
2. Tirfi Tsegaye (Ethiopia) 2:21:19
3. Olena Shurhno (Ukraine) 2:23:32
4. Filomena Chepchirchir (Kenya) 2:24:56
5. Fate Tola (Ethiopia) 2:25:14
6. Alevtina Biktimirova (Russia) 2:28:45
7. Caroline Chepkwony (Kenya) 2:30:34
8. Anna Hahner (Germany) 2:30:37
9. Sonia Samuels (Britain) 2:30:56
10. Degefa Biruktayit (Ethiopia) 2:33:27