The visitors took the lead when Theo Robinson swivelled in the home penalty area before firing past Scott Carson.
Chris Brown doubled their advantage with a near-post header before Wigan’s Shaun Maloney curled in a free-kick.
Leon Barnett thrashed in a late leveller but Doncaster almost snatched victory when substitute Billy Paynter hit the woodwork.
FA Cup holders Wigan are highly-fancied to make an instant return to the Premier League after their relegation last season and have shown their intent with a host of impressive summer signings.
But, since a 4-0 opening-day win at Barnsley, their early days in the Championship have been far from straight-forward.
After a shock 1-0 defeat at Bournemouth last weekend, Latics boss Owen Coyle stressed the importance of Wigan’s home form being the platform for a successful season in the build-up to his first game at the DW Stadium.
But it looked like the Scot, who replaced Everton-bound Roberto Martinez during the close season, was going to suffer defeat against League One champions Doncaster.
The Latics started brightly as they attacked the visitors with a swagger, new signing Grant Holt heading over the crossbar before seeing his instinctive near-post volley parried by Rovers goalkeeper Ross Turnbull.
Ex-Norwich striker Holt, one of Coyle’s most eye-catching signings, was proving a handful and felt he should have been awarded a penalty after he was bundled to the ground by Doncaster right-back Reece Wabara.
Wigan continued to press with Chris McCann slicing through the centre of the Doncaster defence, only to fire straight at Turnbull, before Shaun Maloney’s cross-shot deceived the ex-Chelsea goalkeeper to cannon off the post.
But Doncaster took a shock lead when Robinson, who joined from Derby County last week, netted his second goal in as many appearances with a clinical finish. And it got better for the visitors when Brown nodded in Bongani Khumalo’s cross from close-range.
Wigan were booed off at half-time and almost conceded a third goal within seconds of the restart when Khumalo crashed a header against the post.
But the home side cranked up the pressure and were handed a lifeline through Maloney’s strike after substitute Marc-Antoine Fortune was fouled on the edge of the penalty area.
Doncaster defended for their lives in the final stages and looked set to hold out – but were denied by Barnett’s late strike from 12 yards.