The midfielder was in the right place at the right time to tap home from close range with 56 minutes on the clock after Brad Freidel palmed out Shaun Maloney's corner from under his crossbar under pressure from Arouna Kone.
Try as they might, the lads couldn't carve out a clear-cut chance to equalise as Wigan defended their lead.
Andre Villas-Boas made seven changes to the team that started against Norwich City in the Capital One Cup on Wednesday.
Brad Friedel, William Gallas, Jan Vertonghen, Tom Huddestone - in for the 300th match of his club career - Sandro, Aaron Lennon and Jermain Defoe all returned and Emmanuel Adebayor was back on the bench after injury.
Clint Dempsey had a couple of sighters at goal in the first 10 minutes but it was quickly apparent that Wigan's 5-2-3/3-4-3 system would cause problems.
The front three of Maloney, Kone and Franco Di Santo stopped us building from the back and when we were on the ball, the visitors filtered back goal-side, suffocating the space in the final third.
Jan Vertonghen almost broke the deadlock with a spectacular volley on 22 minutes. He watched a clearance from Gareth Bale's corner over his shoulder and conneced sweetly with his right foot from 22 yards, Al Habsi collected well down to his left with Defoe ready for any spillage.
We were forced into a change a minute later as Sandro limped off, Gylfi Sigurdsson a straight switch in central midfield.
The visitors were clearly growing in confidence and forced Friedel into two fine saves in the space of five minutes.
First, Kone played a one-two with Maloney and struck a firm shot from 18 yards near enough for the goalkeeper to parry to his right and then, on 34 minutes, the same two combined as Kone played in Maloney who beat the offside flag but couldn't beat Friedel one-on-one.
Steven Caulker's header looped just wide but Wigan were soon on the attack again as Maloney dummied for Watson to fire wide from the edge of the box.
Into the second half and Al Habsi saved comfortably from Dempsey's curler but then Wigan grabbed the lead.
Maloney hit an inswinging corner from Wigan's left, Friedel just got above Kone to clear but the ball fell to Watson, who planted his shot home despite the efforts of the goalkeeper.
Adebayor soon entered the fray in place of Defoe and Vertonghen's left foot connected again on the hour, this time Emmerson Boyce got in the way of a goalbound effort.
Al Habsi palmed away Bale's 25-yarder and then Caulker looped a header from Bale's deep corner over the goalkeeper to the far post, where James McCarthy headed away.
We searched in vain for that one, clear-cut chance and crosses from both flanks flashed across the box but Wigan always seemed to have an answer defensively.
Tom Carroll replaced Kyle Walker in the 79th minute, his debut for us in the Premier League.
Indeed, the next effort of note was Maynor Figueroa's free-kick that zipped just wide.
Our final chance fell to Bale from Huddlestone's clipped pass but the winger had to take his shot early and fired straight at Al Habsi.
Spurs (4-2-3-1): Friedel; Walker (Carroll, 79), Caulker, Gallas, Vertonghen; Huddlestone, Sandro (Sigurdsson, 23); Lennon, Dempsey, Bale; Defoe (Adebayor, 57). Unused subs: Lloris, Dawson, Naughton, Falque.
Wigan (5-2-3): Al Habsi; Boyce, Ramis, Caldwell, Figueroa, Beausejour; McCarthy, Watson; Di Santo (Gomez, 70), Kone, Maloney. Unused subs: Pollitt, Jones, McManaman, Boselli, Stam, Lopez.
Goal: Wigan - Watson (56)
Yellow cards: Spurs - Dempsey (46). Wigan - Figueroa (49).
Referee: Mr M Atkinson.