Teenage winger Aaron Lennon fired home the winner after bursting into the area just before the hour mark, moving Spurs on to 65 points with one game to play and within touching distance of a place in the Champions League qualifying round.
Fifth-placed Arsenal are seven points behind Spurs, although they still have three games left starting at relegated Sunderland on Monday.
Tottenham will definitely finish fourth, their best performance since the 1989-90 season, if they win at West Ham United on the final day of the season next week.
If Arsenal win their Champions League final against Barcelona, however, Martin Jol's side would be bumped out of next season's competition, a fact not lost on a number of Spurs fans inside White Hart Lane wearing Barca shirts.
"We played better in the second half although it was still difficult," Tottenham boss Martin Jol told Sky Sports.
"We needed a bit of genius from the little fella (Lennon) and he did it."
BOLTON DOMINANT
For a long time on Sunday it looked as though Bolton would seriously undermine Tottenham's hopes of playing in Europe's premier club competition.
They completely dominated the first half as they strove to revive their own chances of qualifying for the UEFA Cup.
Japanese midfielder Hidetoshi Nakata thumped an early effort against the inside of the post after a knock-down by Jared Borgetti and Ivan Campo also shot over from close range.
Tottenham hung on until halftime and were much better after the break. Danny Murphy looped a volley narrowly over the bar and Lennon blazed over after cutting in dangerously.
The next time Lennon had a chance he made no mistake. Running on to Michael Carrick's pass inside the area, he skipped past a tackle before burying a shot inside the far post.
Bolton responded and should have got a penalty when Stelios Giannakopoulos was brought down by Michael Dawson, who was also lucky to escape a handball incident as Spurs hung on grimly.
"We had clearly enough chances to have put the game beyond Tottenham in the first half," said Bolton manager Sam Allardyce, who added that the defeat had "killed" his team's chances of qualifying for Europe next season.
The main issues in the Premier League were decided on Saturday.
Chelsea wrapped up a second successive title with a 3-0 victory over Manchester United while Birmingham City and West Bromwich Albion were both relegated along with Sunderland.
