Paynter was on hand to convert from close range in the 34th minute when Kelly Youga's looping header from a corner by Eddie Johnson struck the underside of the bar.
He struggled to celebrate his vital strike after being hurt inside the opening minute by a crunching challenge from Brighton defender Adam El-Abd.
Paynter required lengthy treatment and it seemed as if he would be unable to continue, but he battled through until he was substituted in the closing stages.
Brighton began the game brightly enough, Zesh Rehman heading over from a free-kick by Sam Rents and Bas Savage forcing Donovan Ricketts into a good save with a downward header from a cross by Jake Robinson.
Ricketts came to Bradford's rescue within three minutes of them taking the lead when he got the faintest of touches to a looping header from Seagulls captain Guy Butters, to deflect it against the upright.
Substitute Alex Revell went close to equalising for the home side twice in quick succession in the second half.
He turned away from David Wetherall, Bradford's caretaker manager, from a low cross by Rents to clip a shot against the top of the crossbar.
Revell then volleyed over when Robinson pulled a cross back to him at the near post.
Brighton have now won only one of their last 11 matches at home and failed to score in seven of the last nine.
He struggled to celebrate his vital strike after being hurt inside the opening minute by a crunching challenge from Brighton defender Adam El-Abd.
Paynter required lengthy treatment and it seemed as if he would be unable to continue, but he battled through until he was substituted in the closing stages.
Brighton began the game brightly enough, Zesh Rehman heading over from a free-kick by Sam Rents and Bas Savage forcing Donovan Ricketts into a good save with a downward header from a cross by Jake Robinson.
Ricketts came to Bradford's rescue within three minutes of them taking the lead when he got the faintest of touches to a looping header from Seagulls captain Guy Butters, to deflect it against the upright.
Substitute Alex Revell went close to equalising for the home side twice in quick succession in the second half.
He turned away from David Wetherall, Bradford's caretaker manager, from a low cross by Rents to clip a shot against the top of the crossbar.
Revell then volleyed over when Robinson pulled a cross back to him at the near post.
Brighton have now won only one of their last 11 matches at home and failed to score in seven of the last nine.