A speeding driver fleeing a Long Island traffic stop was shot by a state trooper yesterday — but kept on running and was finally caught as he tried to hijack a motorcycle, authorities said.

Troopers tried to pull over Allen Nelson Jr., 49, on Sunrise Highway in Bay Shore, but he continued driving, police said.

A short distance away, he got a flat tire, and when he stepped out of his 2009 Hyundai Sonata, he assaulted a trooper, who fired back in self-defense, officials said.

Nelson, struck once in the shoulder, managed to run off and allegedly tried to grab the motorcycle.

But during the ensuing scuffle, the trooper was able to subdue him.

Nelson was charged with assault, attempted robbery, resisting arrest and unlawful fleeing.