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Gillingham’s long unbeaten run in the league was ended by a former player.
The Gills looked to have rescued a point when Regan Charles-Cook scored late on to cancel out Joe Pigott’s effort but Reilly struck a 90th minute winner.
Steve Evans’ side went into the game 15 unbeaten, the Dons being the last team to inflict a defeat over them, with a fortuitous 1-0 win back in November.
Scott Wagstaff scored the vital goal that day and was one of four former Gills players in their line-up on Saturday. Wagstaff almost put the Dons ahead at the end of an opening half which they had edged, finding no way past Jack Bonham after being played in another Priestfield old-boy Luke O’Neill.
It had been a half that struggled for quality, not helped by a number of stoppages and a reluctance from the visitors to show any haste when restarting play.
Pigott - who scored the winner when the sides last met at Priestfield - had a couple of deflected shots in the half but it was his lobbed effort that came close to breaking the deadlock early on. He beat Jack Tucker to a ball over the top but his dinked shot was acrobatically cleared by Max Ehmer.
It needed a vital block from Ehmer to also deny the striker later in the half.
Tempers on the sidelines were a little more heated than the play, with visiting physio Stuart Douglas angered at suggestions from the home side that Mads Bech Sorensen was play acting when twice going down with a head injury, stopping the Gills in their tracks.
Gillingham reached the break rather fortunate to still be level and brought on winger Jordan Graham for the second half.
But the Gills found themselves behind shortly after the restart, with Pigott turning the ball home after Bonham’s save from Kwesi Appiah’s header fell invitingly into his path.
Gillingham responded well to going a goal behind and had appeals for a penalty waved off by the referee after Tom O’Connor went to ground in the box.
John Akinde - returned to the XI for the weekend match - had a downward header turned around the post by keeper Joe Day and strike partner Brandon Hanlan got free in the box soon after but was unable to pick out a team-mate.
Wimbledon had a great chance to double their advantage when Appiah chased onto a ball over the top but when the cross came in, Pigott somehow put the ball over from a yard out.
The Gills lost captain Max Ehmer to a shoulder injury, leaving them down to 10 men after using all of their substitutes, but they levelled shortly after when Charles-Cook headed in from close range. Day had initially saved well from Hanlan but the substitute was there to nod in the equaliser.
Wimbledon got back infront with a last minute goal, helped by Gills’ lack of numbers at the back.
Bonham did well to make a double save to deny Pigott and then Adam Roscrow but Reilly - who left the Gills after spending pre-season there under Evans - fired the loose ball home to give the relegation threatened side a vital boost.
Tucker came close to a stoppage-time leveller but Day saved his close-range header.
Reaction: We got what we deserved
Gillingham: Bonham, Fuller, Ogilvie, Ehmer, Tucker, Jones (Willock 62mins), O'Connor (Charles-Cook 72mins), O'Keefe, Lee (Graham 46mins), Hanlan, Akinde. Subs not used: Walsh, Mandron, Roberts, Pringle.
Wimbledon: Day, O’Neill, Reilly, Thomas, Sorensen, Wagstaff, Hartigan, Guinness-Walker, Appiah (Roscrow 76mins), McLoughlin (McDonald 90mins), Pigott. Subs not used: Trott, Pinnock, Rudoni, Lamy, Sanders.
Attendance: 4,893 (653 away)