The win restored the Latics seventh place with 41 points, which keeps their hopes of reaching the UEFA Cup alive. Hull lie 13th on 33 points.
Steve Bruce started with Mido and Hugo Rodallega upfront, keeping top scorer Amr Zaki on the bench for the second game running.
Mido made way for Zaki late in the game, but the latter didn’t pose much of a threat during his brief introduction.
Rodallega's Pace
Wigan came close to scoring a bizarre opener in the second minute, when Maynor Figueroa's attempted cross from 40 yards hit the bar.
The home side then sustained more pressure using Mido's aerial ability and Rodallega's pace.
The strike partners combined well in the 15th minute, but Mido blasted the Colombian's fine layoff over Matt Duke's bar.
On the half-hour mark, the lively Rodallega once again set up a nice headed ball for Mido, but the Egyptian couldn’t deliver from close range.
Hull lost defender Andy Dawson to injury before half time, while Bruce had to take off Charles N'Zogbia and bring on Daniel de Ridder after the break.
Five minutes after the interval, Manchester United's on-loan forward Manucho saw his point-blank header brilliantly saved by Chris Kirkland at the near post in what was Hull's best chance of the game.
At the other end, Rodallega looked more impressive than Mido for the Latics, which prompted Bruce to bring on Zaki at the expense of his Egypt mate.
Shortly after Zaki's introduction, Rodallega hit the post with a header, after which his overhead kick hit the Zak before going inches wide.
Wigan finally got their precious winner six minutes from time when Watson capitalized on Duke's poor punch to lob the Hull keeper cunningly, scoring his second goal in two games.