The Bantams had come from two goals down and seemed to have done enough to earn a share of the spoils.
But with just a minute left on the clock Bowditch, a 70th minute substitute, finished a fluent counter attack to keep Brighton's recent revival going.
In contrast Colin Todd's Bradford have now not won in six games and have claimed only one point out of the last 15.
A Bradford side low on confidence started brightly enough with Ben Parker, Dean Windass and Jermaine Johnson all having an early sight of goal.
But it was the visitors who struck first when striker Alex Revell beat City's offside trap. He was slid in by teenage midfielder Dean Cox and poked the ball past the on-rushing Donovan Ricketts with barely quarter-of-an-hour gone.
That goal knocked the stuffing out of Bradford who struggled to find any fluency in a scrappy first-half.
City's hopes of a first win since September took a further blow just two minutes after the re-start when Bradford captain David Wetherall was adjudged to have tripped Brighton's man-of-the moment Jake Robinson.
Seagulls skipper Dean Hammond stepped up to confidently send Ricketts the wrong way.
City fans must have feared the worst after last week's capitulation at Blackpool, but the home side were given a lifeline when they were awarded a spot-kick of their own.
Kerry Mayo handled under pressure from Eddie Johnson and Windass fired in his eighth goal of the season.
Bradford poured forward in hope of an equaliser and came close when Wetherall's header was cleared of the line. When the ball was played back in Steve Schumacher was on hand to volley into the corner of the net with only ten minutes left.
But just as it looked as though the points would be shared, Bowditch, on loan from Ipswich Town, sent the 479 visiting fans home happy.
Revell led the breakaway and played in an inviting low cross and Bowditch slid in to claim the points.