Micky Adams defended John McCombe after a tackle from the Port Vale captain left Northampton's Alex Nicholls with a broken leg.
Nicholls opened the scoring for the Cobblers before his replacement Louis Moult condemned Vale to a 2-0 defeat.
"All my thoughts are with Alex Nicholls at the moment and everyone connected with Port Vale wishes Alex a speedy recovery," said Adams.
"But I've just seen the tackle and it's a genuine attempt by John [McCombe] to win the ball and it's an unfortunate accident.
"John is distraught about it. He is as honest as the day is long and it was genuine attempt to clear the ball after Robert Taylor has put Chris Neal in trouble with the back pass."