The Gills only needed a point to seal the League Two title and established a comfortable advantage inside 23 minutes thanks to Deon Burton's neat volley and a header from former Dons striker Danny Kedwell.
However, Jack Midson halved the deficit with 25 minutes remaining and Jonathan Meades then slotted home a late equaliser for the relegation-threatened Dons.
It leaves the club in the drop zone going into their final-day clash at home to Fleetwood, just one point from safety with as many as seven sides battling for survival.
"I thought there was only going to be one winner at the end," Ardley said. "All we needed was one ball dropping to the right player at the right time, but ultimately the players gave it all they could.
"At this stage of the season it would have been great if we had got all three points, but it was always going to be a tough call because playing the champions away from home is not easy.
"I'm really disappointed with the first half, we worked so hard all week looking at how we were going to go about the game, and then we did completely the opposite.
"We changed the shape for the second half, we stirred them up and to be completely honest, I couldn't have asked for any more than the response we got.
"If we can play like we did after the break next week, we can stay up. I still believe that even though we've only picked up a couple of points in the last few games, we've not been playing badly."