The summer signing had scored in Latics colours before, but that strike against Sheffield Wednesday is not in the record books after the game was abandoned in heavy rain last month.
It was fitting then that after Ben Watson and Aaron Wilbraham had traded strikes, the heavens opened once more as Republic of Ireland international McClean fired in a 78th-minute winner.
Wigan had gone ahead just before half-time through their FA Cup hero Watson, whose name will forever be synonymous with this competition for the header in last year’s final which famously defeated Manchester City at Wembley.
This Sunday will also mark five years to the day Palace sold Watson to the Latics, and he made sure the anniversary will be one to remember with the opening goal 36 minutes in.
The Eagles brought on Dwight Gayle and Wilbraham after the hour to complete their substitutions and, minutes later, they were level when the latter stabbed in from a scrappy corner.
It was the journeyman striker’s first goal since August 2012 but the end of McClean’s own drought proved to be more significant.
The winger, who last scored 12 months ago when at Sunderland, drove through the rain and drilled the ball inside Julian Speroni’s near-post.
There was a welcome sight on the visitors’ team-sheet with Palace club captain Paddy McCarthy, out since April 2012 because of a groin injury, back in the starting line-up.
The inclusions of both Cameron Jerome and Marouane Chamakh suggested plenty of attacking intent, although the former’s most notable act of the opening 45 minutes was to get booked for diving.
Ali Al Habsi had produced a fine stop to deny Jason Puncheon, yet the hosts looked more threatening with McClean, McManaman and Watson all off target with well-hit efforts before they broke the deadlock.
McClean rolled the ball into Roger Espinoza’s feet down the left flank and continued his run, which allowed the Honduran to flick the ball around the corner. McClean was patient in waiting for runners and Watson did not need to break stride as he side-footed into the corner.
There was no chance for Wigan to build momentum or the Eagles to fire straight back as thoughts instead turned to Parr’s serious-looking injury.
Although McManaman was adjudged to have fouled the full-back, it appeared to be nothing more than a coming together. However, Parr clearly had a problem and was on the turf for eight minutes before being taken off.
That led to an extended period of stoppage-time, during which McManaman drew Speroni into a smart stop and the 22-year-old went close again after the break when he lashed wide.
At the other end, Watson let a near-post corner through, which Al Habsi pushed clear with his body, and the keeper was needed again to tip Puncheon’s rebound over the top.
The contest was now becoming more stretched and Pulis threw on Wilbraham and Gayle for Jerome and Chamakh.
It took just four minutes for the changes to pay dividends as Wilbraham levelled on 69 minutes. Barry Bannan’s corner should have been dealt with at the near post but Gayle’s run caused confusion and Wilbraham poked home despite Emmerson Boyce’s best efforts on the line.
After Gayle had forced Al Habsi to divert a vicious effort past the post, Latics boss Uwe Rosler initiated a copy-cat double change of his own by turning to Nick Powell and Marc-Antoine Fortune.
Crucially, McClean was not one of those taken off and he picked up Espinoza’s pass before skewing a shot past Speroni.
Gayle appealed for a penalty to no avail late on and McClean missed a one-on-one with Powell free next to him, but it mattered not as the holders marched on.