Mutai set the course record the last time the NYC Marathon was held, in 2011. Sunday's race returned after last year's cancellation because of the destruction of Superstorm Sandy. Security was also heightened after the bombings at April's Boston Marathon.
On a windy morning, Mutai had an unofficial time of 2 hours, 8 minutes, 24 seconds, well off his mark of 2:05:06 set in nearly perfect conditions.
Mutai pulled away around Mile 22 and beat Ethiopia's Tsegaye Kebede by 52 seconds. He's the first man to repeat in New York since Kenya's John Kagwe in 1997-98.
Kebede, the London Marathon champ, clinched the $500,000 bonus for the World Marathon Majors title. South Africa's Lusapho April was third.
On the women's side, Jeptoo trailed Buzunesh Deba by nearly 3½ minutes at the halfway point. But she started making her move as the race entered Manhattan and passed Deba with just more than 2 miles to go.
Jeptoo, the 2012 Olympic silver medalist and 2013 London Marathon Champ, won in 2:25:07 to clinch the $500,000 World Marathon Majors bonus.
The women's race played out almost identically to the last NYC Marathon two years ago. But this time, Deba was the pursued, not the pursuer.
In 2011, Mary Keitany pulled away to a big early lead, and Deba and countrywomen Firehiwot Dado chased her down. Dado, who won that day, was 14th Sunday as the defending champ.
This time, Deba and training partner Tigist Tufa separated themselves right from the start. Deba wound up finishing 48 seconds behind Jeptoo, while Tufa was eighth.
Jelena Prokopcuka of Latvia, the 2005-06 New York champ, placed third at age 37.
American Tatyana McFadden completed an unprecedented marathon "Grand Slam." The 24-year-old Maryland resident won the New York City Marathon women's wheelchair race Sunday after taking the titles in London, Boston and Chicago earlier in 2013. No other athlete has won those four races in the same year.
McFadden also was the 2010 champion in New York. Born with a spinal defect and left at a Russian orphanage as a baby, McFadden was adopted by an American family and got into sports.
Marcel Hug of Switzerland won the men's wheelchair race.
Security was heightened after the bombings at April's Boston Marathon. Bomb-sniffing dogs roamed the course, and barricades limited access points to Central Park.
The ING New York City Marathon spans all five boroughs. The NYPD had eyes in the air, on the water, and thousands of officers posted along the route. Authorities also had access to 1400 private sector cameras if necessary.
Security was tight from the moment the runners arrived on Staten Island. They were corralled into long bag-check lines, and officers and volunteers repeatedly reminded them to keep cellphones out.
"Security is 100 percent tougher than what I've seen at other races," said Chris Patterson of Rochester, N.Y., who was signed up for New York last year and ran Boston in April.
Elizabeth Hutchinson of Seattle recalled the joy at the starting line in Boston this year. People were handing out sunscreen, Band-Aids and energy gels with a smile.
On Staten Island, she said, "the machine guns are very visible."
"The atmosphere is so different," she said, "It kind of makes me sad."
Charles Breslin, who lost his home in the storm and was volunteering at the marathon, welcomed the race's return.
"I don't know how the rest of Staten Island feels about, but it can only be a good thing," he said. "You have to get back to normalcy."
As the professional women approached Central Park, only a sprinkling of onlookers stood at the police barricades. Ginny Smith, a Manhattan resident who comes to watch each year, said she felt "very frustrated."
Three hours after she first arrived at the park, she was finally allowed to walk in. At Columbus Circle, near the 26th and last mile of the route, police kept her waiting for two hours.
"It was difficult, it was horrible - for something that's basically for the people," she said. "It's unbelievable; you would think there was a war in the city."
Ashley O'Brien of Brooklyn was ready with a bullhorn to cheer members of her running group, the Hudson Dusters. She got teary-eyed remembering the events of the past year.
"It's a nice time to all come back together," she said. "You still remember why it was canceled last year and you remember Boston. So it's a little bittersweet."