The Egyptian striker's 11th goal of the season sealed a third consecutive victory for Steve Bruce's side, who moved up to seventh.
It was Andy O'Brien who gifted Latics the win when the Wanderers defender bundled over Henri Camara in the area a minute before half-time.
And Zaki coolly sent Jussi Jaaskelainen the wrong way for his fourth successful spot-kick of the season and second in three days after scoring in Wigan's 2-1 victory against Newcastle on Boxing Day.
Just two points and one place separated the two sides before kick-off and Wanderers received a major let-off on 23 minutes when Danny Shittu, in for the injured Gary Cahill, brought down Emile Heskey just inside the penalty area, but referee Phil Dowd, incredibly, waived away his protests.
Kevin Davies should have given the home side the lead moments later, but the forward took an eternity on the edge of the six-yard box, allowing Paul Scharner to get back and make the challenge after the defender had failed to cut out Johan Elmander's cross.
Jaaskelainen saved with his feet from Heskey after another Shittu blunder, but that was to be the England player's last involvement after he pulled up with a problem with his hamstring and was replaced by Henri Camara on 33 minutes.
The Latics substitute nearly scored with his first touch after Kevin Nolan carelessly surrendered possession, but Jaaskelainen made a fine finger-tip save to keep out his curling effort.
The Wanderers goalkeeper came to Bolton's rescue again when he saved low down from Lee Cattermole and was then grateful when Titus Bramble shot straight at him.
But the visitors were ahead a minute before half time after O'Brien needlessly bundled over Camara in the penalty area as the striker looked to get on the end of Wilson Palacios' cross. Zaki made no mistake from the spot.
Shittu thought he had equalised nine minutes after the restart, but his header from Matt Taylor's corner was cleared off the line by Palacios with the Wanderers players adamant it was a goal.
Latics keeper Mike Pollitt then denied Elmander with his feet and then Davies' follow-up effort clipped the outside of the post.
And Shittu nearly salvaged a point in injury time, but the big defender's header hit the crossbar as Gary Megson's side slumped to their fourth defeat in five games.