Harry Redknapp's men should have been out of sight at half-time in Saturday's Premier League clash but they only had two early efforts to show from 45 minutes in which they were totally dominant.
A neat 49th-minute finish from Mohamed Diame thrust the Latics back in to contention and, despite Steve Gohouri's 63rd-minute red card, Roberto Martinez's men threatened right to the end.
Van der Vaart stepped in to replace Jermain Defoe after the Spurs striker picked up a virus, with Sandro also coming in for Niko Kranjcar in the only other change to the side that thumped Liverpool 4-0 last weekend.
Martinez made two changes from the 3-1 loss at Everton, with Diame and Gohouri in for the injured Hugo Rodallega and Adrian Lopez.
Spurs looked sleek from the start and came close in the opening minute when Scott Parker found Kyle Walker on the right and his cross was bundled clear by James McCarthy.
And Harry Redknapp's men grabbed the lead in the third minute when Emmanuel Adebayor pounced on Maynor Figueroa's awful back-pass, beat Gary Caldwell and crossed for Van der Vaart to sweep home.
The visitors were looking devastating in the opening minutes and Adebayor once again carved the home defence apart with a through-ball to Bale, whose effort was cleared.
Then moments later Walker delivered another pinpoint pass to Adebayor, who blasted his rising shot just over the bar when he should have scored.
Wigan were having a nightmare, and Spurs should have capitalised again on eight minutes when Ali Al Habsi panicked into clearing a back-pass straight to Parker, who was closed down.
The hosts finally fashioned their first chance in the 12th minute when Jordi Gomez delivered a free-kick from the right and both Diame and Victor Moses were close to connecting.
Spurs' seemingly inevitable second goal arrived in the 23rd minute when Bale was left unmarked in the box and was able to flick home Luka Modric's right-wing corner.
The Wales winger almost repeated the feat in an identical move five minutes later as the inept Wigan rearguard showed no signs of learning from their mistakes.
As Spurs continued their relentless pressure, Adebayor fed Bale who burst in from the left and drilled a low shot which was saved well by Al Habsi on the half-hour.
Martinez swapped Jordi Gomez for Ronnie Stam at the break and his side started the second half with more purpose, a dangerous Moses cross booted out of the six-yard box by Younes Kaboul.
And Stam was instrumental in the Latics reducing the deficit on 49 minutes, pouncing on a poor Benoit Assou-Ekotto clearance to feed Diame, who twisted and fired a superb low shot past Brad Friedel.
With the game suddenly wide open, Spurs poured forward straight from the restart and Adebayor drove in a low shot which was blocked by Al Habsi.
Wigan looked like a different team, with Moses suddenly incisive on the left flank, Diame bossing centre-field and Caldwell almost setting Franco Di Santo clear with a pinpoint pass.
But their revival threatened to be cut short in the 63rd minute when Gohouri was sent off for a second bookable offence after hacking down Bale.
Modric had a hopeful penalty appeal waved away by referee Jon Moss in the 68th minute and the action quickly swung to the other end, where Friedel saved comfortably from Moses.
Martinez made a double substitution on 73 minutes with Conor Sammon and James McArthur replacing Di Santo and Ben Watson as Wigan sought an improbable draw.
Kaboul almost made sure of the points for Spurs six minutes from time when he bulleted in a free-kick which struck the Wigan wall and clattered the bar.
There was still time for the Latics to launch a series of late assaults, with McArthur coming close from long range and Sammon miscuing a shot in the box, but they could not find the equaliser.