Holt was bemused he failed to win a 15th-minute penalty after being hauled down by Reece Wabara and Rovers made the most of their fortune.
Theo Robinson fired in his second goal since joining five days ago and then Chris Brown headed home just before the break.
Bongani Khumalo would have made it three but for the woodwork and their lead was soon halved thanks to Maloney's clever free-kick.
It seemed as though the visitors would hang on yet Marc-Antoine Fortune's cross was stabbed in by Barnett, although the three points would have been going back to south Yorkshire had the crossbar not denied substitute Billy Paynter moments later.
With Doncaster believed to be on the verge of new investment, chairman John Ryan was sat in the directors' box.
He was perhaps casting an envious glance at counterpart Dave Whelan's summer recruits, particularly Holt, who nodded over early on from six yards.
The hosts were causing problems and a wonderful move involving Emmerson Boyce and Maloney culminated in Holt firing against Turnbull's leg.
Wigan were incensed when Holt was somehow denied a penalty after Wabara got the wrong side of the ex-Norwich forward and dragged him down.
Doncaster had few answers to Holt and when he sent McCann clear Turnbull produced a fine one-handed save before Maloney's cross-cum-shot struck the woodwork.
However, it was one of the visitors' target men who would strike first after 25 minutes.
A long free-kick landed at Robinson's feet and, with his back to Barnett and the goal, he squeezed the ball between Scott Carson and the post.
Turnbull was called upon again, this time to repel Boyce, yet Paul Dickov's men would double their advantage two minutes before the interval.
Khumalo's deep cross was nodded across goal by central-defensive partner Rob Jones where Brown, wearing a bandage after an earlier clash of heads, was on hand to plant his effort past Carson.
Coyle responded by introducing Fortune at half-time, although it was Rovers who would almost strike again as Khumalo's terrific header crashed against a post.
Fortune proved to have an impact 12 minutes after arriving, though, winning a free-kick when Jones tripped him on the edge of the area.
Both Maloney and James McClean presided over it and it was the former whose effort dipped over the wall and dropped into the bottom corner of the net.
Jean Beausejour was then introduced to provide service yet Holt, Fortune and Boyce could not find the target with headers from his centres.
Holt's growing frustration became evident when he pushed Dickov as he tried to quickly restart.
But that frustration, shared by the DW Stadium crowd, soon turned to elation as Fortune pulled the ball across for Barnett to expertly rifle home.
Paynter came on for Rovers before play restarted again and he almost made the ultimate impact, guiding his header on to the top of the crossbar with Carson beaten.
- Sports & Recreation
- Shaun Maloney
- Ross Turnbull
- Grant Holt
- Emmerson Boyce
- Reece Wabara
- Bongani Khumalo