Josip Skoko pulled one back with the last kick of the game but, while the Royals climb to within a point of a UEFA Cup spot, Paul Jewell's side are perilously close to the Premiership drop zone.
Wigan made a blistering start and took the game to Reading from the first minute making a mockery of their abysmal run of form.
They were almost ahead inside two minutes when new £500,000 signing Caleb Folan flicked the ball into the path of Lee McCulloch, who saw his shot flash inches wide of a post.
Reading failed to heed the warning and 60 seconds later the Latics were ahead.
A long punt from the back invited Heskey to run ominously into the space between Reading's two centre-backs and the former England man unleashed a clinical finish inside Marcus Hahnemann's near post from the edge of the box.
Reading finally snapped into life midway through the half and Glen Little's hanging cross from the right sat up invitingly for Lita only for the striker's downward header to bounce wide.
Steve Sidwell then posted a contender for miss of the season, poking wide of an open goal after Chris Kirkland had dropped Little's cross right at the midfielder's feet.
Sidwell looked to the referee to spare his blushes by awarding a foul against the goalkeeper but referee Steve Bennett seemed to indicate a goal kick.
Instead it was defender Ingimarsson who got Sidwell off the hook by heading the home side level on 31 minutes.
Wigan continued to drive forward positively though and McCulloch saw a stinging drive beaten away acrobatically by Hahnemann after more good hold-up play by Heskey.
Reading dominated the second half but always looked vulnerable to Wigan's bold attacking instincts with stand-in centre back Andre Bikey a tower of uncertainty at the heart of the Reading defence.
But the home side did get their noses in front when Long nodded them ahead six minutes into the second half.
Lita did well wide on the right and fed Little whose cross should have been headed home first time by Long.
The striker failed to connect full with his header but Kirkland's flap fell at the feet of Hunt who did well to lob the ball back to the far post where Long was able to beat David Unsworth to the header.
Reading's attempts to sew the points up saw them bring on substitute Dave Kitson for his first home appearance since injuring his knee on the first day of the season.
The striker should have made it 3-1 within minutes of his belated arrival, but blazed over a gaping goal after Kirkland had blocked Hunt's effort with his legs.
Kitson though did play a major part in Reading's crucial third goal when he stooped bravely to win a header as Kirkland came to meet him and allowing Lita to steer home the loose ball.
The Latics did have the last word when Skoko poked home at the near post after Hahnemann had spilled a Ryan Taylor free-kick, but the last kick of the game came too late to prevent another defeat.