A goal in each half made it a miserable return to Fratton Park for Paul Cook.
Brett Pitman’s 40th-minute penalty and Jamal Lowe’s 55th-minute effort saw Pompey move to within goal difference of the League One play-offs with a 2-1 win.
Wigan failed to move to the top of the table as the Blues had an evening to enjoy in front of the Sky cameras.
Will Grigg’s 89th-minute header did make it edgy, however, through five minutes of stoppage time.
For much of the afternoon it was a fairly low-key first Fratton visit for the man who guided his side to a memorable League Two title.
Cook did get a ticking off from the referee, however, and was subjected to some light-hearted ribbing about the scoreline.
It was a big win, though, which means it’s now undoubtedly game on for the play-offs.
Pompey threatened within two minutes as Gareth Evans’ cross from the right was met by Brett Pitman, but his first-time effort was blocked.
It was the captain who provided the dangerous ball in after 18 minutes but Jamal Lowe’s outstretched leg couldn’t meet his delivery.
Wigan’s penalty appeals were ignored after 28 minutes as Michael Jacob went down under the attentions of Anton Walkes.
But the Blues did get the chance to make the breakthrough from the spot against the run of play five minutes before the interval.
Ben Close was the man adjudged to have been fouled by Dan Burn and Pitman emphatically sent Walton the wrong way.
It should have been two just three minutes later, as Callum Elder failed to clear and Pitman went clear but Walton was equal to his finish.
The second goal did arrive 10 minutes after the restart as Nathan Thompson’s cross was controlled and then finished on the turn by Lowe in the six-yard box.
From there the Blues found themselves on the back foot but threw bodies at the ball at every opportunity.
McGee made a great stop to deflect Nick Powell’s finish on to the bar with 21 minutes left.
The keeper then excelled himself with an outstanding reflex stop to his left to keep out Will Grigg’s 10-yard volley, which looked a certain goal.
Grigg made it a nervy finale when he headed in former Blues midfielder Gary Roberts’ cross in the 89th minute.
Pompey held on through the late drama, though, to ensure scenes of celebration on the final whistle.