Rowett said: "You could see from my response at the end how I felt about it all.
"Five minutes went up, we then had one substitution, but for some reason the game carried on and they got their goal after seven-and-a-half minutes.
"You could argue that Wimbledon deserved a point for their effort and endeavour, but to get done like that is particularly galling."
Kee made up for missing from the spot at Oxford a week earlier by drilling home a 21st minute penalty after strike partner Dominic Knowles had been upended by Dons skipper Alan Bennett.
But the visitors got stronger and looked threatening the longer the came went on and substitute Jack Midson hit a post before Jones snatched a point for the visitors.
Rowett said: "It's disappointing because I can talk about how we didn't play well, but it looked as though we'd seen the trouble out.
"We needed to defend the corner better, but it looked as though we'd dug in to get what would have been a magnificent three points - which is what it's all about at this stage of the season.
"To get done on 97 and a half minutes means we're not a very happy bunch because those two points could make all the difference at the end of the season."
- Sports & Recreation
- Darren Jones
- Billy Kee