Lee Collins poked home 20th-minute opener when he raced on to Darren Carter's free-kick - Northampton's first away goal of the season.
Stuart Dallas made sure of Northampton's second league win of the season with 16 minutes remaining as he scored a fine solo goal to double the visitors' lead.
Matt Duke made a fine save to deny promotion-chasing Wimbledon's Harry Pell an injury-time consolation, but the Dons slipped to their first home defeat of the season.
"We played well, had loads of opportunities, loads of crosses, but never looked like we would get on the end of it," Ardley said.
"It's not so much creating chances that's important, it's about getting in the box, timing runs and getting on the end of it. It didn't matter how many we got in, we weren't going to get any in.
"We switched off, the same players have done it a couple of times this season, it's cost us a goal. It's not good enough.
"I don't mind losing games, we're not going to go through the season without losing games. When you do lose, it's about how you bounce back. I thought for 20 minutes we fought back quite brightly.
"Next week is going to be tough, they're all tough. There's no givens. The coupon buster is always there."