A man who allegedly opened fire in a subway car during rush hour, striking two people, including a teenager he’d gotten into an altercation with on the moving train, was arrested on Tuesday, police said. 

Alexander Villafana, 20, of Brooklyn was charged with two counts each of attempted murder, assault, criminal possession of a weapon and reckless endangerment for the Nov. 28 shooting on a Manhattan-bound C train, cops said.

The accused gunman and a 17-year-old boy got into an argument on the train as it headed toward the Ralph Avenue stop, at around 5:40 p.m., according to police.

Villafana then allegedly whipped out a gun and squeezed off several shots — striking the teen in the left hand and hitting an innocent bystander, a 57-year-old man, in the left ankle, cops said.

The gunman ran off after firing the shots, police said.

The teen was brought to Bellevue Hospital and the older victim was taken to Kings County Hospital, both in stable condition.

The shooting disrupted the evening commute, causing the C train to run express for two hours, skipping the Ralph Avenue stop where police were investigating.

The suspected shooter was on the loose until Tuesday morning when investigators picked him up at his home in Cypress Hills, cops said.

Villafana was awaiting arraignment in Brooklyn Criminal Court later Tuesday. 

“With hundreds more cameras being installed every month inside subway cars, it’s never been clearer that anyone targeting New Yorkers in transit will be identified, caught, and brought to face justice,” NYC Transit President Richard Davey said in a statement following the suspect’s arrest.

“I’ve said before that we’ve got more cameras than a Las Vegas casino and as this case demonstrates, they are positioned to assist investigators when necessary,” Davey added.

Additional reporting by Nolan Hicks