A second away win of the season for Roberto Martinez's side was completely deserved as Spurs struggled to make the most of a positive start and had to listen to the jeers of their own fans for long spells of the game.
They controlled the early tempo but had only a Clint Dempsey shot, deflected behind for a corner, to show for their almost complete dominance of possession.
Spurs came closest to taking the lead on 20 minutes when a corner fell for Jan Vertonghen, but the Belgian defender's sweet volley was well held by Ali Al-Habsi.
Wigan grew into the game and had a decent chance of their own just before the half-hour when Arouna Kone and Shaun Maloney linked up well and Kone forced Brad Friedel into a fine reaction save.
Friedel came to the rescue again moments later when Maloney beat the offside trap only to see his shot bounce back off the keeper as he spread himself as wide as possible.
Watson wasted a decent chance just before the break, firing over after more good work from Kone, and the jeers from sections of the home support when the half-time whistle went told the story from Spurs' point of view.
The goal Wigan threatened as the opening half wore on came 11 minutes after the break when Friedel failed to clear a Maloney cross under pressure from Kone and Watson volleyed home from six yards.
Spurs upped the pace, as they clearly had to, and almost forced an equaliser on 68 when Steven Caulker headed a corner back across goal but James McCarthy headed off the line with Al-Habsi beaten.
The home side continued to struggle in the final third despite bringing on some fresh blood and Wigan threatened on the break with Kone's greediness costing them a chance and Maynor Figueroa not far off target with a long-range free-kick.
Gareth Bale curled a set-piece of his own just wide as the seconds ticked down, but despite plenty of late pressure an equaliser was not forthcoming and Wigan headed back to Lancashire with three valuable, and hard-earned, points.
Spurs had come in to the game having won five of their last six Premier League matches, but they were desperately poor this afternoon.
The home fans knew that with games against Manchester City and Arsenal coming up, this had been a perfect opportunity to register three more valuable points after last weekend's morale-boosting win over Southampton.
The supporters also turned against Villas-Boas 10 minutes into the second half when he substituted Jermain Defoe for Emmanuel Adebayor.
Loud boos rang out at White Hart Lane and the home fans chanted the name of the England striker, who sauntered off the pitch before going down the tunnel.
|Tottenham Hotspur||Team Statistics||Wigan Athletic|
|0||1st Half Goals||0|
|5||Shots on Target||3|
|3||Shots off Target||3|
|51.9||1st Half Poss.||48.1|
|46.5||2nd Half Poss.||53.5|