Stoke substitute Whelan was the unlikely hero when he came off the substitutes bench and fired the winner with just five minutes left on the clock to record their first away win of the season.
The away side almost broke the deadlock after just two minutes. Matthew Etherington created space on the edge of the box and his shot was superbly cleared by Jonathan Woodgate, who showed all his bravery when he clashed with Ricardo Fuller to stop the ball crossing over the line.
The home side fought their way back into the game and created their first major chance on 11 minutes when Niko Kranjcar's cross picked out Peter Crouch, who towered above the Stoke defence and saw his header produce a fine save from Steve Simonsen diving away to his right.
The defensive problems for Redknapp continued on 13 minutes when Woodgate was forced to leave the pitch with concussion following his goal-line clearance in the opening minutes.
Simonsen was clearly not affected by his late call-up to the Stoke side and kept City in the game with another fine save to deny Aaron Lennon's curling right-foot shot.
The home side continued to create the best openings and were unlucky not to open the scoring on 26 minutes when Lennon's cross fell to Crouch, whose header was cleared off the line by James Beattie.
The woodwork then denied Tottenham 60 seconds later when Kranjcar fired a low shot which beat Simonsen in the Stoke goal but the ball struck the post.
Stoke clearly came with a game-plan to frustrate the home side and Tottenham were finding it hard to break down the visitors' defence.
Redknapp's side came close again on 48 minutes when Robbie Keane's low shot was parried away by Simonsen.
Crouch looked certain to knock the rebound home, but Ryan Shawcross and Andy Wilkinson were on hand to knock the ball away.
The Tottenham manager knew he needed to change things around and brought on both Roman Pavlyuchenko and Jermaine Jenas as he looked to break the deadlock.
But the Stoke defence stood up to everything that the Spurs forwards threw at them and showed once again why they are such a tough team to break down in the top-flight.
Redknapp must have known it was not going to be his day when Lennon was forced to leave the field through injury and the home side were down to ten men.
And he was given the worst possible anniversary present when Whelan fired the crucial matchwinner on 86 minutes.
Stoke substitute Fuller forced his way past Benoit Assou-Ekotto and played the ball in to Whelan, who seemed to have all the time in the world inside the area.
Whelan made no mistake striking the ball past Heurelho Gomes into the corner of the net to make it an enjoyable trip back to the Potteries.