Lhota, the former head of the Metropolitan Transit Authority, led the race from start to finish, fending off the self-financed bid of billionaire grocery store magnate John Catsimatidis. George McDonald, head of the nonprofit DOE Fund to help the homeless, finished a distant third.
Lhota was a deputy mayor under Rudolph Giuliani and was praised for steering the MTA through Superstorm Sandy. He resigned to run for mayor and led the polls throughout the campaign.
He will face the Democratic nominee, likely Bill de Blasio, on November 5.
The candidates are vying to replace Mayor Michael Bloomberg, who is leaving office after 12 years.