In favourably cool conditions with a light wind, Cheruiyot, clocked two hours, five minutes and 52 seconds as he crossed the finish line, holding off Ethiopians Tekeste Kebede and defending champion Deriba Merga.
Cheruiyot said he wanted to stick with Merga, who broke from a large pack of men's runners at mid-race.
"If somebody is a champion, you try to go with them," said the 21-year-old, who broke Robert Kipkoech Cheruiyot's previous course record of 2:07:14 set in 2006.
Ryan Hall led at the halfway mark before finishing fourth in 2:08:41, the fastest time for an American.
"My goal going into the race were to have fun and to run free," Hall said.
In the women's race, Erkesso built a big lead going into the final few miles but was reeled in by Russia's Tatyana Pushkareva, who set up a furious sprint down Boston's Boylston Street to the finish line.
Erkesso won by three seconds in 2:26:11. Last year's winner, Kenya's Salina Kosgei, was third.
The Ethiopian said she attempted to drive the pace from the start, fearing that other runners had stronger finishing kicks.
"I knew the Russian lady was coming from behind me. 'She doesn't pass me today,' I'm thinking in my mind," Erkesso said. "I didn't believe I would win it until the very end."
Results: Men: Robert Cheruiyot (Ken, 2hrs 05mins 52secs) 1; Tekeste Kebede (Eth, 2:07:23) 2; Deriba Merga (Eth, 2:08:39) 3; Ryan Hall (US, 2:08:41) 4; Meb Keflezighi (US, 2:09:26) 5.
Women: Teyba Erkesso (Eth, 2hrs 26mins 11secs) 1; Tatyana Pushkareva (Rus, 2:26:14) 2; Salina Kosgei (Ken, 2:28:35) 3; Waynishet Girma Tafa (Eth, 2:28:36) 4; Bruna Genovese (Ita, 2:29:12) 5.
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