And the £6million striker repaid the manager's confidence as he set the Latics on their way to their best Premiership win so far by smashing in his third goal of the season with just 63 seconds on the clock.
But it was defensive mistakes that proved most costly to City, who were beaten 4-3 in the corresponding fixture last season.
They were looking to find the cure to their travel sickness, having taken just one point on their travels, while Wigan's priority was to get clear of the relegation zone after a stuttering start to the season.
City were still well below strength, but they had Darius Vassell back on bench and were further boosted by the return of goalkeeper Nicky Weaver after a back injury.
They also gave debuts to teenagers Matthew Mills and Michael Johnson.
Despite last week's home defeat against Manchester United, Paul Jewell refused to panic, and settled for just a couple of changes. Australian midfielder Josip Skoko got his first start, taking over from Denny Landzaat, and Antonio Valencia replaced Gary Teale.
Former Hearts defender Andy Webster made his debut on the bench after his protracted move from Scotland.
For Wigan it was a dream start, and an absolute nightmare for City who were two down inside the opening four minutes.
The Latics took just over a minute to get off the mark with Heskey starting the goal spree.
Emmerson Boyce supplied the cross from the right which took a slight deflection off Georgios Samaras and the former Liverpool striker crashed a shot past Weaver.
That was bad enough for City, but it suddenly got a whole lot worse.
They gave away a free-kick to the left of the area and Skoko arrowed it into the box. There seemed to be little danger but Blues skipper Richard Dunne was left red faced after he turned a header into his own net.
Bernardo Corradi was on target with a header to signal the start of a spell of City pressure, but there was another anxious moment for the Blues when a Kevin Kilbane corner whistled across the face of goal after Weaver failed to cut it out at the near post.
The visitors missed a terrific chance to pull one back when Trevor Sinclair picked out the unmarked Corradi with a great cross, but he put the header over the bar.
Wigan were inches away from a third when the impressive Paul Scharner flicked a header just over, before City were furious to have a penalty appeal ignored with Paul Dickov leading the claims of handball against Leighton Baines.
Vassell came off the bench and was desperately unlucky not to pull one back for City when his shot trickled just wide.
But it became mission impossible for Stuart Pearce's men when Wigan conjured up two more goals in a three-minute spell.
Kilbane's weighted pass was perfect for Baines as he raced into the box, and the left-back - another England tip - did well to turn it inside where Henri Camara beat Stephen Jordan to the punch.
Wigan struck again when Valencia was allowed to race into the box and smash a fierce right footer past the helpless City keeper to hammer the final nail into the visitors' coffin.