The game started off brightly for the home side, with Beausejour coming close with two efforts and Ivan Ramis seeing his header cleared off the line.
However, the Hornets were first to take the lead on 36 minutes when Lewis McGugan took on his man on the right-hand side and found the far corner.
It took just four minutes for the Latics to equalise, as Beausejour headed the home side level.
Just before the hour mark, Waghorn was able to turn and send a low strike into the bottom right corner to put his side in the lead.
The home side cranked up the pressure throughout the rest of the second half, with Beausejour continuing to threaten, while Ikechi Anya had two efforts for the beleaguered Hornets towards the end of the game.
The result puts Wigan in sixth place with a game in hand on the other sides in the playoffs, while Watford remain in mid-table, occupying 12th place.