Makau finished more than a minute outside the record in a time of two hours five minutes and eight seconds, with compatriot Geoffrey Mutai second, two seconds behind, and 20-year-old Ethiopian Bazu Worku third in 2:05:25.
In the women's race, Aberu Kebede finished a minute ahead of pre-race favourite and fellow Ethiopian Bezunesh Bekele, to win with a time of 2:23:58. Japan's Tomo Morimoto was third.
Kenyan trio Makau, Mutai and Eliud Kiptanui had set their sights on Gebrselassie's world record of 2:03:59 set on the same course two years ago. Makau's winning time of 2:04:48 in Rotterdam in April, where Mutai came second, was the fourth fastest ever.
The Kenyan trio's split time after 10km on Sunday was just seven seconds slower than Gebrselassie's 2008 world record time at the same stage but the bad weather took its toll and at the halfway mark they were more than half a minute off.
Kiptanui then peeled off as his countrymen powered on, joined by Ethiopian Worku, running the flat Berlin course in pouring rain. The three athletes worked their way through the final kilometres before Worku fell some 20 metres behind with two kilometres to go and Makau held on for first spot just past the German capital's iconic Brandenburg Gate.
Results: Men: Patrick Makau (Ken, 2:05.08) 1; Geoffrey Mutai (Ken, 2:05.10) 2; Bazu Worku (Eth, 2:05.25) 3.
Women: Aberu Kebede (Eth, 2:23.58) 1; Bezunesh Bekele (Eth, 2:24.58 ) 2; Tomo Morimoto (Jpn, 2:26.10) 3.
