Ben Close livened up a dull first half with a fine strike on a wet and windy Boxing Day afternoon on the south coast.
Lyle Taylor hit back with a penalty just after the break, only for Brett Pitman to net a spot-kick of his own to secure the points for the Blues.
Kenny Jackett made one change from the side that were beaten at Shrewsbury before Christmas.
It came in attack, where Matty Kennedy dropped to the bench to make way for Conor Chaplin just behind lone striker Pitman.
Both sides had perhaps indulged themselves a tad too much the previous day, with the first half limping along.
Pompey enjoyed the majority of possession and territory, but George Long was largely untroubled in the Dons goal.
It was actually the visitors who were first to threaten, with Cody McDonald – perhaps put off by Luke McGee’s presence – poking the ball wide of the post.
Close sent a couple of dangerous deliveries into the box, only for the Londoners’ back-line to deal with them both.
A snap-shot from the returning Chaplin was well-struck on 19 minutes, but the ball flew straight at Long.
The lively Gareth Evans also had an effort that flew narrowly wide, as the contest struggled to move out of second gear.
Pompey fans were finally given reason to sit up and take notice when Chaplin’s shot took a deflection and hit Jamal Lowe.
He was unable to adjust his feet quickly enough, however, with the ball ricocheting off the winger and being saved by Long.
A couple of Wimbledon corners caused hearts to flutter at the other end, but it was the hosts who finally forged ahead just before the break.
Lowe slide in to win back possession and feed CLOSE, whose 25-yard effort skimmed off the wet surface and into the bottom corner.
AFC Wimbledon 0
The mood was buoyant inside Fratton Park at the break, but it soon soured when the visitors levelled just after the restart.
There was plenty of controversy about the goal, however, with AFC Wimbledon awarded a penalty after the ball bounced up and struck Christian Burgess on the arm.
Referee Craig Hicks decided it was deliberate and Taylor smashed the resulting penalty into the roof of the net.
There was growing frustration from fans and players alike, as a few more decisions started to go against them.
Jackett made a double switch just past the hour mark to try to inject some fresh impetus into his side.
Chaplin and Lowe were the men to make way, with Oliver Hawkins and Kennedy coming on to replace them.
Hicks looked to have ensured he was off next season’s Christmas card list for anyone living in Portsmouth, but the official was soon back in the home side’s good books.
He spotted Barry Fuller’s shove on Pitman inside the box and, much to the delight of the Fratton faithful, pointed to the spot.
It was PITMAN who stepped up to take the penalty and confidently sent Long the wrong way with a thunderous finish.
Wimbledon almost hit back, as an angled drive from former Blues winger Andy Barcham flashed across the face of goal.
But Pompey saw out the closing stages with relative ease to ensure a return to winning ways in League One.
Pompey (4-2-3-1): McGee; Thompson, Burgess, Clarke, Haunstrup; Close, Rose; Evans, Chaplin (Hawkins 64), Lowe (Kennedy 64); Pitman (c)
Goals: Close 45, Pitman 72 (pen)
Subs not used: Bass, Donohue, May, Bennett, Main
AFC Wimbledon (4-4-2): Long; Fuller (c), Oshilaja, Charles, Meades; Trotter, Soares (Kaja 78), Abdou, Barcham; Taylor, McDonald
Goals: Taylor 50 (pen)
Booked: Soares, Barcham, Fuller, Trotter
Subs not used: McDonnell, Nightingale, Kennedy, Hartigan, Egan, Francomb
Referee: Craig Hicks
Attendance: 18,644 (728 away fans)