Newcastle claimed the points from a thrilling game to put a dent in Tottenham's Champions League hopes.
Bowyer's goal gave Newcastle the perfect start
Lee Bowyer slid the Magpies ahead after 66 seconds but Robbie Keane headed home Aaron Lennon's cross to level.
Shola Ameobi followed up Nolberto Solano's shot to restore Newcastle's lead before Alan Shearer made it 3-1 from the spot after Bowyer was fouled.
Jermaine Jenas missed an open goal for Spurs before Michael Dawson's red card ended any chance of a fightback.
The Magpies had lost their last four Premiership games against Spurs without scoring a goal but they were quickly on top here.
Charles N'Zogbia ran on to Solano's pass and squared the ball for Bowyer to bundle the ball over the line from close range.
Despite their lofty league position, Tottenham did not seem to be at the races in the early stages and Shearer and Solano had chances to extend the home side's advantage.
But from their first meaningful attack Martin Jol's side found themselves level, Lennon's pace and trickery giving him space on the left-hand side of the area to cross for Keane to instinctively head home.
Newcastle kept coming forward however and they were quickly back in front.
Bowyer's tackle set Solano free and Spurs keeper Paul Robinson could only parry his shot into the path of Ameobi who slotted home.
Things got better for the Magpies when Solano sent a bouncing ball into the box and instead of shepherding it out, Edgar Davids inexplicably barged Bowyer over, giving referee Mike Dean little choice but to point to the spot.
Shearer stepped up to bury his penalty and claim his 19th career goal against Tottenham.
The game almost took another twist before half-time when Keane hammered a shot against the bar after a Jenas free-kick had ricocheted into his path.
But instead Newcastle went in at the break firmly in command, and Tottenham did their level best in the second half to ensure things stayed that way.
Jenas had been greeted on his return to his former club by being roundly booed every time he touched the ball - but his day was to get even worse.
Robbie Elliott's poor back-header set him free in the area and he rounded Shay Given - only to miss the target completely with the goal at his mercy.
Keane grazed Given's post with a low shot soon after to show Tottenham were still in with a shout but any chance of them taking something from the game were ended when Dawson was shown his second yellow card for holding Shearer back.
Newcastle almost added a fourth when Bowyer's header brought a fine save out of Robinson but for the final half hour they remained comfortably in control and Spurs never threatened a recovery.
Newcastle manager Glenn Roeder:
"The players took out their disappointment from last week's defeat at Charlton on what is a very good Tottenham side.
"Three one did not do out first-half performance justice.
"People say there is nothing to play for but there are points and pride - and for our fans we must play this way for the rest of the season."
Tottenham manager Martin Jol:
"We showed many faces here - the first 25 minutes the way we gave goals away was almost unforgivable.
"But in the second half we came back although we were playing with with 10 men for half-an-hour.
"Normally if you play away and you give the motivation to the opponents like we did you can end up losing five or six nil but I think we stood up well."
Newcastle: Given, Carr, Ramage, Moore, Elliott, Solano (Faye 80), Bowyer, Emre (Clark 63), N'Zogbia (Chopra 90), Shearer, Ameobi.
Subs Not Used: Harper, Boumsong.
Booked: Moore, Emre.
Goals: Bowyer 2, Ameobi 25, Shearer 30 pen.
Tottenham: Robinson, Kelly, Dawson, Gardner, Lee, Jenas, Carrick, Davids (Murphy 88), Lennon (Defoe 70), Keane, Mido.
Subs Not Used: Cerny, Stalteri, Huddlestone.
Sent Off: Dawson (61).
Booked: Dawson, Mido, Keane.
Goals: Keane 19.
Ref: M Dean (Wirral).