Emmanuel Adebayor scored twice as Spurs, a day after manager Harry Redknapp was overlooked for the England job in favour of Roy Hodgson, enjoyed their first away win of 2012.
The result ensured Tottenham remained in fourth place, ahead of Newcastle on goal difference who beat Chelsea 2-0 at Stamford Bridge on Wednesday, and took them to within just a point of third-placed north London rivals Arsenal, with just two games of the season left.
Usually, the top three clubs in England qualify for the Champions League proper, with the fourth-placed side entering the preliminary round. But if Chelsea beat Bayern Munich in the Champions League final at the German club's home ground on May 19, they will take the place that would otherwise go to the team finishing fourth.
Defeat left Bolton in the relegation zone and not even the presence in the stands of Wanderers midfielder Fabrice Muamba, who suffered a cardiac arrest when these teams met in an FA Cup tie in March, could inspire his team-mates to a much needed victory. Bolton keeper Adam Bogdan needlessly spilled a 12th minute effort from distance by Gareth Bale before recovering to superbly deny Rafael van der Vaart from close range.
Six minutes later Aaron Lennon was left frustrated when his goal-bound effort, after exchanging passes with Adebayor, deflected off Mark Davies and fizzed narrowly wide. It looked like being one of those nights for Spurs when van der Vaart's curling 25-yard free-kick fell wide in the 31st minute before Tottenham keeper Brad Friedel was forced into his first save, denying David Ngog with his chest.
The game was opening up and moments after the industrious van der Vaart had again forced a save from Bogdan, Tottenham took the lead in controversial circumstances in the 37th minute. Sandro appeared to handle the ball to win the corner from which Bale teed-up Luka Modric to arrow in an unstoppable 25-yard finish.
Bolton then spurned a glorious chance to equalise in first-half stoppage time when a Tim Ream free-kick was nodded back across goal for Dedryck Boyata, who slashed wildly over while unmarked from eight-yards.
Fortunately for the hosts, Nigel Reo-Coker was not so wasteful.
The 27-year-old former Aston Villa midfielder had only managed to score two goals since joining last summer but he showed wonderful composure to beat Friedel with a low 51st minute volley after a clever flick by Ngog. Suddenly, Bolton were on top for the first time.
Wanderers captain Kevin Davies, who had scored both goals in last weekend's 2-2 draw at Sunderland, went close with a header before a dipping attempt by Chris Eagles which almost had Muamba leaping from his seat. But Bolton's failure to take their chances proved costly as Tottenham sealed victory with two goals in as many minutes.
Van der Vaart restored Tottenham's lead on the hour mark with a terrific first time finish after more good work by Bale before Modric provided the pass of the night which allowed Lennon to square for Adebayor to make it 3-1 from five-yards. There was still time for former Arsenal striker Adebayor to round Bogdan and make it 4-1 - and leave Bolton's Premier League future in a perilous state.