Angelo Balanta's strike confirmed MK Dons' place in the play-offs and pushed Notts County into a relegation battle on the last day of the season.
A driven cross from Peter Leven found Sam Baldock, who converted from close range to put the hosts ahead.
Baldock then turned provider when his low cross was met by Balanta, who poked the ball in to double the lead.
Substitute Lee Hughes pulled one back when he fired home after a Craig Westcarr corner, but the Dons held on.
MK Dons manager Karl Robinson told BBC Three Counties Radio:
"It's what we deserve. We sat down in pre-season and spoke about application, hard-work and endeavour, and all the components you need and they have done that.
"The job isn't done yet. We have to play Oldham next week and have to be professional. We will rest players, I am telling you that now.
"All we can do is prepare right when the play-offs come around. We will train especially for these play-offs. We have started to prepare, now we can implement what we wanted to do."
Notts County manager Martin Allen told BBC Radio Nottingham:
"I thought we played very well. We had a couple of good chances in the first half and they are not in the play-off places for nothing.
"To come away from home - even though they had a lot of possession, which I expected - they never really hurt us. Our team kept a good shape and kept discipline, which is very important to do at this stage of the season and we had a couple of good chances ourselves.
"What you can't do is fault the effort, the commitment, the energy of all the players - everybody who was involved had a go. We just didn't have enough to open them up and create something in the final third. It's a fine line between success and failure."