The substitute climbed off the bench to head home Ronan Curtis’ left-wing cross 11 minutes from time and secure a 2-1 victory for Kenny Jackett’s side.
The Dons’ Joe Pigott had cancelled out Marcus Harness’ opener against the run of play to spark fears the Blues would drop crucial points.
Yet Marquis, who recently scored in 2-1 wins over Fleetwood and Walsall, maintained his hot streak.
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Now Pompey find themselves in seventh, separated from the play-off positions by goal difference.
Marquis said: ‘In the last week we’ve got through two rounds in two cups and won against a tough Wimbledon side who came here to frustrate us and nicked their goal.
‘We started the second half slowly, they nicked their goal, tried slowing everything down, we just had to try to find a way back into the game.
‘I was just happy I was able to come onto the pitch and score what ended up being the winner.
‘I thought we were pretty good in the first half, we controlled a lot of the play.
‘After the break, fair play to Wimbledon, they looked like a different side, they started threatening down the sides of our centre-halves more, they got a foothold in midfield and came alive.
‘It was quite unlike us that we started the second half slowly, I don’t know if the fact we weren’t attacking the Fratton end played a part.
‘They got a goal against the run of play, it was a great ball and a great finish and a bit of a sucker punch which took the wind out of us for another 5-10 minutes.
‘But the gaffer made some changes and the game then swung back into our favour.’