Simon Morgan added the second after the break to cut Reading's lead at the top of the table to two points, Brighton having now played the game in hand.
Zamora broke the deadlock in the 37th minute with his 12th goal in as many home appearances since Peter Taylor took charge last August. He just managed to beat Ian Sampson to an in-swinging free-kick from Paul Watson to head past Northampton keeper Keith Welch.
Northampton's challenge evaporated in the 59th minute when Morgan slotted home his first goal for Brighton. Watson was the provider again with a penetrating low cross which was side-footed in from close range by the former Fulham stopper.Brighton did not have things all their own way at the rain-lashed Withdean Stadium.
Northampton made a nonsense of their lowly position by giving the home side a couple of real scares. Sam Parkin, on loan from Chelsea, glanced a Roy Hunter cross against a post in the 17th minute. Brighton then had Michels Kuipers to thank for preserving their 1-0 lead early in the second half. The big Dutch keeper threw himself to his right to claw away a goalbound free-kick from Jamie Forrester.
Taylor said: "It was a very hard game. Northampton are playing better than their position suggests, so it was a difficult match. "We have got to improve on the way we start matches and some of the individual things we did were not as good as you would like, but we were solid once we got the goal.
"It was a great set piece by Paul Watson for Bobby. "I've looked at Simon Morgan's goals record and it's quite impressive really with the appearances he has made. It was a great finish and a great ball in from Watson."
Morgan said: "It was a tremendous three points. We knew it was going to be difficult but once we broke free we were always confident. "You have got to give Northampton credit. They came and had a real go and it took us a while to settle.
"It is about time I scored. Goals for me have been as rare as rocking horse droppings this season. It was a great cross by Paul Watson in to my stride and it went through the keeper's legs."
Brentford's 0-0 draw at home to Chesterfield leaves Brighton four points clear of them in the second automatic promotion place, but Morgan is taking nothing for granted. "I haven't even thought about automatic promotion yet," he said. "I am just thinking about beating Bury on Saturday.
"We like playing at Withdean. We have four home games left and four wins would do very nicely."