The 34-year-old striker netted his second goal of the season just before half-time to condemn Orient to their fourth straight defeat.
Milton Keynes dominated the first half and Luke Chadwick and Dean Bowditch were both denied one-on-one by keeper Ryan Allsopp, who also spilled a 25-yard drive from Angelo Balanta against the post.
Lowe then had a fierce shot pushed over the bar by Allsopp before the veteran striker put the Dons ahead four minutes before the break, tapping in Bowditch's low cross from close range.
Leyton Orient improved after the interval and David Mooney was denied three times by keeper David Martin within the first 10 minutes of the second half.
The Dons regained control in the closing stages and Chadwick had a low shot brilliantly saved by Allsopp before Lowe fired a snap-shot narrowly wide.