But it needed a last minute save by keeper Chris Kirkland from Leroy Lita to deny Reading a share of the points.
Heskey celebrated his home debut and his 500th career appearance with the first half winner - and with a bit more luck, he might have ended up with a hat-trick.
His 38th minute strike was his first goal in the Premiership with Birmingham City back in February and earlier the former England man had rattled the woodwork with another effort. And in the second half, he was just inches away again after lobbing the ball over the Reading keeper.
But there were also impressive performances from two other Wigan new boys, Dutch international Denny Landzaat and Ecuador international Antonio Valencia, on a season long loan from Villarreal.
Reading's return to the JJB stadium brought back fond memories for Wigan but not for the Royals. They had to suffer in silence as Wigan celebrated a 3-1 win in May 2005 which clinched promotion to the Premiership.
But at least it spurred Reading on to follow the same route 12 months later and set up the first clash between the sides at this level.
Wigan, beaten on the opening day at Newcastle, were unchanged with fit again Pascal Chimbonda on the bench while the Royals - with one win from their two games so far - were missing suspended defender Ibrahima Sonko, sent off at Villa Park in midweek, and striker Dave Kitson, ruled out with knee ligament damage.
Keeper Kirkland, included in the England squad for the European games, was twice in action as Reading got off to a positive start pulling off saves from Bobby Convey and Lita.
But Wigan were looking dangerous when the ball was knocked forward to the lightning fast Henri Camara. Twice Lee McCulloch sent him racing clear with a couple of terrific passes, but first Steve Sidwell and then Sam Sodje got back to deny the Senegal international a strike at goal.
Camara, who has just signed a new improved three-year contract with the Latics, was also involved in the build with Valencia which set up Heskey. But the ex-Liverpool star was caught inches offside.
Wigan suffered a big blow when Camara limped off with a hamstring problem to be replaced by David Connolly. But they twice went close to breaking the deadlock.
Valencia picked out Heskey from a corner, and he thundered the header against the crossbar and Marcus Hahnemann produced a stunning save to divert a fierce shot from the 20-year-old.
But Wigan took the lead after 38 minutes with Heskey getting his first Premiership goal for the Latics since his move from Birmingham.
Landzaat and Connolly set up the chance and Heskey timed his run into the box perfectly to slot the ball beyond the keeper and into the net.
American Hahnemann prevented further damage just before half time showing quick reactions to deny Connolly a shooting chance after McCulloch's flick into the box.
Valencia hammered a free kick high over the Reading bar, and fired wide with another attempt before the visitors went close when Ivar Ingimarsson headed wide from a Nicky Shorey corner.
McCulloch hit another into the side netting, and Heskey lifted one over the bar after Landzaat sent him through on goal as Wigan hunted the killer goal.
With Reading pressing forward looking for an equaliser they were caught on the break with McCulloch playing sub Graham Kavavnagh in on goal but the Irishman's shot came back off the keeper's legs.
Valencia chipped in with a vital clearance at the other end as Reading made it a nail-biting finish for the home fans before the points were finally in the bag after Kirkland's quality save from Lita.