Foy found himself at the centre of another goalline debate as Spurs got a boost ahead of their Champions League play-off second leg at home to Young Boys on Wednesday.
A goal down in that game, Harry Redknapp's side secured the points at the Britannia Stadium on Saturday thanks to a brace from Bale.
In between his efforts, Stoke equalised through Ricardo Fuller and thought they had drawn level for the second time in the dying embers of the game. However, Foy allowed play to continue even though a shot from Jon Walters, on his debut, appeared to go over the line.
He ignored all the protests and despite an encouraging second-half display, Stoke suffered their second successive defeat.
They almost took the lead inside two minutes after good work by Walters following his arrival from Ipswich in midweek.
He made space down the right and delivered the ball into the area. However Michael Dawson made a crucial interception with Fuller ready to pounce.
Tottenham made the breakthrough in the 20th minute with Bale at the heart of things. The Wales full-back cracked in a shot that was blocked by goalkeeper Thomas Sorensen.
Peter Crouch was first to react but his effort came back off Ryan Shawcross. However, to the Stoke skipper's horror, his clearance went straight to Bale who headed home.
Stoke drew level in the 25th minute with Tottenham guilty of poor defending. Younes Kaboul directed Matthew Etherington's corner into the area and Fuller clipped a shot beyond Heurelho Gomes.
Tottenham regrouped and regained their lead in the 30th minute with a stunning second goal from Bale.
Aaron Lennon began the move and got beyond the defence before lofting the ball into the Welshman's path. Bale showed superb technique to crack in a volley from the left that flew over Sorensen and high into the right hand corner of the net.
Tottenham were spraying the ball about well and Bale released Lennon. The winger however took a touch too many and Stoke were able to clear their lines.
Fuller then carved out an opening for himself with a quick turn on the edge of the area which left him with only Gomes to beat.
The Jamaican, though, failed to get enough power on his shot and the goalkeeper made a comfortable save.
Bale then showed a fine turn of pace in first half stoppage time to get to the byline and whip the ball across. But Sorensen twice denied Jermaine Jenas from adding to Spurs' lead.
With Stoke still finding it hard to break the visitors down Pulis introduced Tuncay Sanli in the 64th minute for the ineffective Glenn Whelan.
Then Lennon split the home defence to find Wilson Palacios. He drove the ball across the face of the area but Danny Collins scrambled it away.
Tuncay almost pulled Stoke level with a shot from 25 yards that took a huge deflection. But Gomes somehow got up and turned it over the bar.
Tuncay was then wasteful, heading wide at the far post from Etherington's corner before Shawcross fired a close range shot over the post in a good spell of pressure by Stoke.
Tottenham then hit back with Tom Huddlestone spraying the ball out to Bale. He was on course for a hat-trick but with only Sorensen to beat saw his effort blocked.
Fuller tested Gomes from close range in the 85th minute before the match ended in chaos. Robert Huth's header was punched away by the goalkeeper and Walters was first to react but all their protests were in vain.