Husband Tom Cruise and their daughter, Suri, were at the finish line to congratulate the actress, according to event officials.
Holmes had registered under an alias so she wouldn't draw too much attention to herself, event officials said, but her time was listed in the official results under her real name.
The 26.2-mile course travels through all five boroughs of the city, starting on Staten Island and finishing in Manhattan's Central Park. This year, 39,085 runners started the race.
Paula Radcliffe, of Great Britain, who had a baby just 9 months ago, won the women's race in 2 hours, 23 minutes, 9 seconds. Martin Lel of Kenya won the men's title in 2:09:04.
Holmes has said she has always liked to run, and took it up to help lose baby weight after giving birth to her daughter, who is now a year old.
"I'm good, but I'm feeling very tired," Holmes said.
The 28-year-old actress trained for months for the grueling event.
