Pompey were in ascendency and pushing for a winner in their League One contest at Stadium MK.
They had turned things around after a nervy opening 45 minutes – which saw Gavin Bazunu make a series of fine saves – to look the stronger team.
But MK Dons then broke quickly from a corner and Ethan Robson scored to secure all three points for the hosts.
And Danny Cowley was particularly frustrated that his side failed to respond proactively to falling behind.
The Blues boss said: “At 70 minutes I could only see one winner because we’d wrestled control and had a good place in the game.
“We played with much more belief in the second half and created four really promising opportunities, as well as some other dangerous moments.
"My biggest disappointment was how we responded to falling behind – we stopped doing what we’d been doing well."
“But we didn’t execute our decision making at speed well enough and that’s why we didn’t take those chances.
“We’ve created enough away from home to win the game and have conceded a bad goal, despite working really hard on our defensive transition.
“More than the goal, though, my biggest disappointment was how we responded to falling behind – we stopped doing what we’d been doing well.
“We’ll be rightly criticised for not scoring again, although we got into dangerous areas and need that final action, which defines you. I’ll worry more if we’re not creating anything.”
Pompey can now look forward to back-to-back Fratton fixtures after their four most recent outings came on the road.
Cowley said: “We’re obviously disappointed because we’ve now lost each of the past two matches in the league.
“But we’ve had eight games this season and six of them have been away, so it will be nice to get back to Fratton Park for the next two.”