Scott Fraser bagged the only goal on 41 minutes to ensure the Blues have failed to win their past three games.
And to make matters worse, they’ll be without Jack Whatmough for the next four matches after he was handed a second straight red card of the season.
The first half was a frenetic affair, with both sides having chances.
On 12 minutes, MK Dons struck the post through Matt O’Riley’s left-foot effort from the edge of the box before Andrew Surman’s subsequent shot went just over.
Then O’Riley spurned a big opportunity when he nodded wide when unmarked inside the area.
Marquis almost produced a moment of brilliance in the 16th minute when his acrobatic overhead kick produced a fine save from home keeper Andrew Fisher.
Moments later the striker let fly a speculative effort from the halfway line that almost caught Fisher off his guard but ran wide.
The game continued to ebb and flow, with Ronan Curtis clipping the outside of the post on 31 minutes shortly after Jack Whatmough had denied Fraser a clear-cut chance.
A breakthrough was clearly coming – and it fell to the Dons.
In the 41st minute, Ethan Laird skipped past Charlie Daniels, who brought down the attacker to concede a spot-kick.
Fraser stepped up and tucked home the penalty home with aplomb.
In stoppage-time, Russell Martin’s side almost doubled their advantage but for a block on the line from Daniels.
Then at the death, Marquis had a deflected effort over following a good cutback from Curtis.
The second half started as the first ended – with both sides striking the bar in a matter of minutes.
Shortly after the restart, Fraser hit the woodwork before visiting skipper Tom Naylor’s header from Daniels’ corner resulted in the same outcome.
The game understandly started to calm down after a high-octane hour.
However, Pompey’s chances of getting a result were dealt a major blow when Whatmough was given his marching orders for flying into a tackle two-footed on Harry Darling.
The Blues stay sixth in the table but seventh-placed Charlton are now two points behind with a game in hand.
Danny Cowley’s side have just five matches remaining and head to Swindon on Tuesday.