Kevin Nolan scored the winner 18 minutes from time in a game which the visitors should have won more easily.
Jay-Jay Okocha was the most unfortunate and could have left North London with a hat-trick.
Tottenham went into the game boasting an unbeaten record under caretaker boss David Pleat, but the Spurs players and the home crowd seemed to have next week's North London derby against Arsenal on their minds.
Bolton took control soon after Spurs' only chance of the first half.
On 30 minutes Gustavo Poyet put Robbie Keane through, only for the striker to see his cross shot palmed away by Jussi Jaaskelainen.
But the near miss seemed to galvanise Bolton, who began to thrive because of the classy Okocha.
The Nigerian international struck a thunderous shot with his left foot on 18 minutes only for the ball to crash against the bar.
He then saw a free-kick just go over the bar and Kasey Keller had to be alert to block Per Frandsen's near-post effort.
Tottenham were booed off at half time but things didn't improve after the break.
They pleaded desperately for a penalty when Simon Charlton appeared to handle in the area but referee Uriah Rennie turned it down.
Bolton were still the better team and Okocha struck the bar for the second time when his free-kick deflected off Kevin Davies.
Stylianos Giannakopoulos then saw Keller touch his 25-yard drive on to the bar and out for a corner.
After the resulting kick was cleared to the edge of the area, Okocha's low effort was fumbled by Keller and Nolan turned the ball home.
Okocha still had time to hit the bar with another right-foot special before Sam Allardyce's side secured the three points.
Spurs boss David Pleat admitted Okocha was the difference and said: "It was a very poor performance by us and we are not making any excuses.
"They pressed us well and Okocha was superb."Allardyce added: "When you hit the woodwork four times you wonder if it will be your day. It made it very uncomfortable in the last few minutes.
"But Okocha was inspirational. He decided to turn the magic on after ten minutes and we started to pass it a lot better."