Police responding to Morris Avenue in Farmingville just after midnight encountered the suspects fleeing the scene.
They attempted to drive away in a Chevrolet Equinox, and crashed head-on into a police cruiser, police said.
According to Suffolk County Police Department Assistant Commissioner Justin Meyers, one suspect, who is at Stony Brook University Hospital, will be charged with burglary. Another man, who was bitten by a police K9 during the incident, is being charged with criminal trespass.
The officer who was driving the vehicle that the Equinox hit was not injured.
There were four people in the home at the time of the incident and no one was injured.
Police said the individuals involved are known to one another.