Latics boss Paul Cook's return to Fratton Park was a miserable one as a first-half penalty kick from Brett Pitman and Jamal Lowe's strike after the break were enough to give the home side maximum points.
Wigan created the first chance of the evening in the 10th minute when former Tranmere Rovers midfielder Max Power gained possession in the final third and shot towards the bottom corner, forcing a save out of Luke McGee between the home sticks.
The visitors edged most of the first period but struggled to get their shots on target, with James Vaughan twice failing to test McGee from close range after good build-up play.
The striker had the opportunity to double his side's advantage moments later, gaining possession inside the box and forcing Christian Walton into a reaction save with his right boot, the last meaningful attempt from either side before the referee's whistle.
Wigan were the bookmakers' favourites ahead of the game, but their hopes of staging a fightback were dashed early in the second half when Lowe scrambled Nathan Thompson's cross over the line from close range.
Cook's men produced a late rally in an attempt to make a game of it, but Nick Powell could only find the crossbar when he gave his marker the slip and got a shot away in the closing stages.
The Latics did pull a goal back one minute from time when substitute Will Grigg guided the ball over the line from close range, but Portsmouth held on to keep their hopes of securing a playoff spot alive.
The result leaves them in ninth place in the table, one of five teams on 51 points, while Wigan stay third with games in hand on the top two.
PORTSMOUTH (4-2-3-1): McGee; Walkes, Whatmough, Clarke, Haunstrup; Thompson, Close; Naismith, Evans, Lowe; Pitman
WIGAN ATHLETIC (4-2-3-1): Walton; Byrne, Dunkley, Burn, Elder; Power, Morsy; Massey (Grigg 66') Powell, Jacobs (Roberts 81'); Vaughan