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.

Health Minister Recep Akdag was quoted by the Anadolu news agency as saying traces of one of the decomposition products of Sarin had been detected in the blood and urine of several victims.
At least 89 people were killed in the incident in rebel-held Khan Sheikhoun.
Syria's government has repeatedly denied using any chemical weapons.
The US has rejected the assertion, however, and on Friday it carried out a missile strike on the Shayrat airbase, where it said a Syrian Air Force jet that attacked Khan Sheikhoun with chemical weapons took off.
President Bashar al-Assad's ally Russia, which says the Syrian jet had in fact hit a rebel depot full of chemical munitions, denounced the "illegal action" by the US.
A number of casualties were treated at hospitals in Turkey, which opposes Mr Assad, following last Tuesday's incident in neighbouring Idlib province.
The World Health Organization said their apparent lack of external injuries and similar symptoms, including acute respiratory distress, suggested they had been exposed to organophosphorus chemicals, a category that includes nerve agents.
On Tuesday, Mr Akdag announced that a chemical known as isopropyl methyphosphonic acid (IMPA) had been "identified in the blood and urine tests conducted on samples taken from the victims".
Once exposed to air and water, Sarin breaks down into IMPA and methylphosphonic acid (MPA).
The UN concluded that rockets filled with sarin were fired at several rebel-held suburbs of Damascus in August 2013 after finding traces of IMPA in samples taken from the scene of the attack, which the US blamed on Syria's government.
Earlier on Thursday, Russia's president urged the Organisation for the Prohibition of Chemical Weapons (OPCW) to open a full investigation into last week's incident.
Vladimir Putin also claimed rebels were planning "acts of provocation" using chemical weapons to encourage further US strikes on government forces.
A Russian military spokesman said that the Syrian government was prepared to allow OPCW experts to visit the Shayrat airbase to search for chemical weapons.

The incident happened on Wednesday at about 18:00 in Wardieburn Place West.
The men, aged 43 and 45, had travelled from Aberdeen. They were attacked in a stairwell by two men who are then thought to have left by the back of the block.
Both victims suffered serious injuries and the 43-year-old man is in a critical condition.
Police are appealing for witnesses.
The first attacker is white and aged 17-19.  He has a Central Scotland accent and light-coloured short hair, which is shaved at the sides.
He was wearing a light-coloured sky blue hooded sweatshirt and grey jogging bottoms.
The second attacker is a white man in his mid-20s. He has a stocky build and was wearing a striped top.
Det Ch Insp Stuart Houston, of Police Scotland, said: "This was an appalling attack on two men who came to the address in good faith.
"This attack happened in daylight and we believe there may be a number of witnesses who may have seen the suspects in the area.
"Anyone with information that can help with our inquiries is urged to contact police immediately."
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.
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Turkey says it has "concrete evidence" the nerve agent Sarin was used in a suspected attack by Syrian government forces a week ago, state media report.
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An investigation has been launched into the attempted murder of two men who had travelled to Edinburgh to buy a car.