Bolton looked to have booked their passage into the next round after a Ledley King own goal and a penalty from Jay-Jay Okocha had cancelled out a fine effort from Jermaine Defoe but defender Goran Bunjevcevic struck for Spurs with just minutes on the clock.
Both sides as expected made changes to the teams which came together in the Premiership at the weekend. Bolton included Julio Cesar, Tal Ben-Haim, Fernando Hierro, Henrik Pedersen and Kevin Poole in the starting eleven whilst Spurs gave run outs to Kasey Keller, Sean Davis, Reto Ziegler and the afforementioned Bunjevcevic. There was also a recall for England striker Jermain Defoe who took the place of Robbie Keane.
In all fairness the home side had started off the better team and where managing to gel quickly into a game which for the first stages was played at a lesser pace than normal. Bolton had their first chance on seven minutes when Kevin Davies managed to out muscle the Spurs defensive duo of Ledley King and Noureddine Naybet to get a shot in on goal. Unfortunately for the former Southampton striker his shot sailed right into the arms of the American goalkeeper Kasey Keller.
A few minutes later Davies missed a glorious chance to open the scoring when he failed to connect to an excellent curling cross from the right by the on loan El-Hadji Diouf.
On 27 minutes the game came into full swing when Bolton were awarded a free kick. Spanish veteran Fernando Hierro curled the ball into the box from the left hand side and England defender Ledley King was to get the final touch on Henrik Pedersen's goalbound header to open the scoring for the Trotters.
Hierro then tried to get in on the scoring act himself but his drive was well saved by Keller who was celebrating a rare start at the expense of Paul Robinson who was rested.
Shortly before half time Spurs tested the Wanderers goal for the first time as Mali international striker Freddie Kanoute forced veteran goalkeeper Kevin Poole into a save from close range with a header.
With just a minute to go till the interval the London side found themselves on level terms thanks to an excellent goal by Defoe. Welsh midfielder Simon Davies played the ball in from the right and the English striker Defoe produced an all in one movement on the turn and the resulting shot flew past Poole from the edge of the area.
Shortly after the interval Hierro had another chance to double Bolton's goal tally for the evening but the Real Madrid legend saw his effort sail high and over into the family stand.
On 56 minutes Bolton's Henrik Pedersen found Keller on top form with the former Leicester City man denying the Dane a chance to increase his goals tally for the season with a fine low save.
Hierro then added further strikes to the statistics column but was to find a mix of good goalkeeping and inaccurate shooting standing in his way from making it 2-1 to Bolton.
With just over a quarter of an hour remaining in normal time Pedersen was to miss the best chance of the match as he blased over from Diouf's right wing cross. The Dane was unmarked in the area but somehow managed to get the ball over the bar when it seemed easier to score but a couple of minutes later Bolton got their reward for some pressure in the Spurs half.
A high ball into the box caused problems for the Spurs defenders and although Pedersen won the header for Bolton referee Mike Dean had adjudged that the striker had been pulled back by defender Goran Bunjevcevic. Nigerian midfielder Jay-Jay Okocha comfortably despatched the resulting penalty into the left corner of the goal.
Spurs were not done yet and they made similar strides in the second half as they had done in the first half and were keen to attack the Bolton defence in the closing stages. With five minutes to go Julio Cesar cleared the ball out for a Tottenham corner and defender Bunjevcevic found himself unmarked to steer Robbie Keane's right wing cross past Kevin Poole slightly against the run of play.
The late drama at the Reebok Stadium meant that the tie was to go into extra time and this was to severly test both sides who has served up a good game in the league just a few days ago.
Five minutes into the first period of extra time Spurs took the lead thanks to a header from substitute Michael Brown. Fellow sub Michael Carrick had floated in a ball from the left from all of 35 yards leaving the ex-Manchester City and Sheffield United player Brown to steal in for his first goal of the season.
Wanderers skipper Jay Jay Okocha then saw an excellent diagonal volley from the edge of the area bounce just wide of Keller's far post but the extra time period seemed to favour Santini's men.
The 103rd minute saw Tottenham further increase their advantage as Defoe scored his second of the contest. A backpass from Nigerian midfielder Blessing Kaku was way too short for Bolton keeper Poole and this allowed the nimble Defoe the chance to make it 4-2 to Spurs.
Bolton could feel the game slipping from their grasp but where given hope when former Spurs favourite Les Ferdinand planted a fine header past Keller to make the scores 4-3. Ferdinand had rose well to head home a fine cross from the Bolton full back Nicky Hunt.
Ferdinand was to later hit the post with a further header as the Bolton side pressed agonisingly in search for yet another goal but one was not forthcoming. Even keeper Kevin Poole went up in the dying seconds to try and salvage the game for the Trotters but this was all done in vein as ref Mike Dean blew for time.
An exciting game for the neutral but Bolton will feel aggrived at not holding onto the match in normal time when in control. Spurs however produced a fine comeback and extra time display which ultimately proved the deciding factor.