Goals from Tal Ben-Haim and Kevin Davies gave Wanderers their first double of the season after Spurs had battled back with an equaliser from substitute Jermain Defoe.
El Hadji Diouf had given the Trotters the lead with an early second-half penalty after Erik Edman had handled.
But Spurs' hopes of taking anything from the game evaporated when Freddie Kanoute was sent off for a second bookable offence.
Spurs could have been a goal up in the fifth minute after Ivan Campo had been caught dawdling on the edge of his own area. Kanoute was quick to steal the ball but placed his shot just wide of the post.
Spurs' display of pace certainly kept Wanderers on the back foot in the opening quarter.
Robbie Keane was quick to test the home back four with a turn of speed through the middle while Kanoute was quick to seize on any scoring opportunity and went close again with a header that was only inches too high.
Spurs had also done their homework in defence as well, Ledley King and Timothee Atouba keeping a tight reign on Davies.
That, however, allowed Diouf to find space and he looked the most likely in the opening quarter to get through on goal, although Paul Robinson was never really tested.
He was called into action in first-half added time, dealing with a swerving free-kick from Kevin Nolan and a Davies header.
Within three minutes of the re-start however, Wanderers were ahead.
Edman, under pressure from Davies in the packed area handled the ball, referee Mike Dean pointed immediately to the spot and for the second successive Premiership game, Diouf converted the penalty, firing powerfully past Robinson.
Spurs' protests were long and loud, the referee finally losing patience and booking both King and Kanoute for dissent.
Once they had regained their composure they almost snatched the equaliser, Jussi Jaaskelainen having to produce a good save to tip a Michael Brown thunderbolt over the bar, then knocking a shot from Stephen Kelly round the post.
Suddenly the game had burst into life and Robinson had to react first to keep out a snap shot from Ivan Campo.
Spurs brought on Defoe in the 65th minute and within three minutes he had put them level.
A mistake by Ben-Haim let in Keane and when Ricardo Gardner missed the ball, Defoe was quick to push the ball through Jaaskelainen's legs.
Four minutes later, Spurs were reduced to ten men when Kanoute brought down Anthony Barness and received his second yellow card and his marching orders.
As Spurs reverted to placing Keane in a solo role upfront, Wanderers took off defender Barness and replaced him with Khalilou Fadiga.
That gave the home side more attacking scope and Diouf should have done better when he shot wide in the 82nd minute, but in the 87th minute Wanderers finally broke Spurs' resistance.
Ben-Haim headed in a Stelios Giannakopoulos corner before Diouf's brilliant through ball gave Davies the home side's third goal in the 88th minute.