The powerful core of the storm, with the most intense winds, passed overnight between St. Martin and the U.S. Virgin Islands, said Lixion Avila, a hurricane specialist with the U.S. National Hurricane Center.
"It could have been worse," Avila said. "They were very, very lucky."
Hurricane Omar had maximum sustained winds of 125 mph but a last-minute shift to the east meant that St. Croix, the most populated of the U.S. Virgin Islands, experienced the weaker side of the system. Winds there reached just 48 mph mph, officials said.
The storm knocked down trees, caused some flooding and minor mudslides but there were no immediate reports of deaths or major damage, said Mark Walters, director of the U.S. Virgin Islands disaster management agency.
The nearby British Virgin Islands also emerged largely unscathed, said Deputy Gov. Inez Archibald, noting there was little damage beyond some mudslides and scattered debris.
"We did reasonably well actually," Inez told The Associated Press. "We did not get what we expected."
Early Thursday morning, Omar was centered about 160 miles northeast of the Northern Leeward Islands. It was moving northeast near 30 mph and had maximum sustained winds of 115 mph.
Omar was taking an unusual southwest-to-the-northeast track toward the central North Atlantic, well away from the U.S. mainland.
On the Puerto Rican island of Vieques, which was brushed by the storm, people returned to their homes from shelters where they spent the night and awaited the resumption of ferry service to the mainland of the U.S. island territory. Lingering bands of the storm were expected to bring rain and rough seas.
"Everything was calm, nothing happened," said Joselyn Ponce of the local office of emergency services.
One death was reported on Puerto Rico's tiny island of Culebra. Authorities say a 55-year-old man collapsed from cardiac arrest while trying to install storm shutters on his house.
Many people throughout the islands had feared the worst and spent Wednesday securing their homes and making sure they had enough food, water and batteries.
"I plan to stay up all night and ride out the storm, but I have a feeling it's going to be very bad," said St. Croix resident Helino Cruz, retiree from the island's giant Hovensa oil refinery.
The refinery, one of the 10 largest in the world, shut down operations for the storm. Hovensa was expected to conduct an inspection for any damage before deciding whether to restart the refinery.
Hurricane Omar forced at least three cruise ships to divert course. Flights were canceled on several islands.