The patient was taken from his home by the Lebanese Red Cross and into quarantine at a Beirut hospital after early symptoms appeared, the ministry statement said. His condition appeared to be stable, it said.
The previous two cases in Lebanon had been tied to an earlier flight from Iran that arrived last week carrying 150 passengers.
Iran said on Thursday its death toll from coronavirus had risen to 26 and the total number of infected people now stood at 245, the highest number of deaths from the virus outside China.
As the virus spreads in the Middle East, several Arab countries have suspended flights and imposed shipping restrictions.