The weather ensured there was never any chance of the 25-year-old breaking the top Berlin marathon time set by Haile Gebrselassie two years ago when he ran the 42.195 kilometre stretch in 2 hrs 3 minutes and 59 seconds.
Yet despite the constant rain, Makau finished in 2 hours, 5 minutes and 8 seconds, securing the first Kenyan victory in the German capital. Bazu Worku from Ethiopia was third, 15 seconds behind Makau.
"Berlin is my city," said Makau. "I just don't like the weather."
The women's race was won by Aberu Kebede in 2 hours, 23 minutes and 58 seconds, ahead of compatriot Bezunesh Bekele and Japan's Tomo Morimoto.
The best German runner was Sabrina Mockenhaupt, who came fourth with a personal best time of 2 hours, 26 minutes and 21 seconds.
"It was really difficult, the start was much too slow. I gave everything towards the end but it was not enough. I am satisfied though," she said.
Nearly 41,000 other runners also braved the miserable conditions to slog through the city, with the inevitable fancy dress competitors lending some colour to the day and earning cheers from the thousands of spectators who lined the route.
Gebrselassie did not take part this year, having competed in the Great North Run last year in preparation for the New York Marathon on November 17.