Alex Jones scored his seventh of the season as Port Vale recorded their first away victory of the season.
Bruno Ribeiro brought back Anthony Grant and Kjell Knops while Sebastien Amoros came in for the suspended Paulo Tavares.
The home side had the first chance when Alnwick saved well from Agard and then Bowditch’s effort was saved by Alnwick.
On the half-hour mark Lewington hit the post after Vale failed to clear their lines but then Lewington gifted Vale the lead when he handballed in the box. Alex Jones saw his penalty saved but netted the rebound for his seventh of the season.
Vale had a chance to double their lead just before the break when they broke but Amoros’ drive went wide. Then a fine run by Sam Hart saw his effort deflected wide.
Vale took a goal lead into the break and the second-half started quietly. On the hour mark Alnwick made another good save from Bowditch as the home side pressed.
The Vale were on the back foot for much of the second period but Milton Keynes were mostly reduced to long-range efforts. In the Vale defence, the back four and keeper were coping well under the pressure.
However, the Valiants were dangerous on the break and one attack forced a good save from the keeper after good work from Jones. A goal would arguably have sealed the win but instead Vale had to hold out as the home side pressed with Alnwick again saving well from Colclough.
In injury time a Ben Reeves free-kick rattled the bar with Alnwick beaten but despite that pressure, the Valiants held on to record a clean sheet and an excellent first away victory of the season in front of the television cameras.