The man said he shot at their car after they refused to stop when he challenged them on Saturday. They were not hurt.
He said that earlier he had heard the pair say "did you get anything"?
Police in Florida have used the incident as an opportunity to issue guidelines for teenagers and parents on safely playing the game.
Police say they received a call from the parents of one of the teenagers when it was noticed later that bullets had caused a flat tyre, News4jax reported.
The parent said the teenagers did not realise they were being shot at, and thought that the man was only trying to scare them.
The guidelines issues by the Flagler County Sheriff's Office include best practice tips for Pokemon Go players. They advise players to:
The sheriff's office also advises parents of Pokemon Go players to:
According to data from SimilarWeb, people are now spending more time playing Pokemon Go than they are on Snapchat, Instagram and WhatsApp.
The game has also been installed on more Android smartphones in the US than the dating app Tinder.
Two teenagers playing Pokemon Go late at night in their car in Florida were shot at by a householder who mistook them for burglars, police say.