Roman Pavlyuchenko gave Harry Redknapp a timely reminder of his talents by firing in a brilliant 20-yard free-kick.
Pavlyuchenko blasted home an early contender for goal of the season with a powerful strike that flew in off the bar, just 24 hours after Redknapp admitted he would consider selling the striker in the January transfer window.
Surprise starter Heurelho Gomes did well to deny Gokdeniz Karadeniz in the first half, and Tottenham were second best for most of the second half, but they held on to register the win that moved them two points clear at the top of Group A.
Hardly a classic game, Spurs looked poor and their play was disjointed at times, but the Londoners now head to Russia for the return fixture next month with a comfortable cushion at the top of the table thanks to one moment of brilliance from Pavlyuchenko.
With Redknapp intent on keeping his first-team regulars rested for Sunday's game at Blackburn, Pavlyuchenko was given a chance to push his case for a regular slot.
Redknapp gave out mixed signals about Pavlyuchenko's future on Wednesday, praising the big Russian striker while admitting that he would reluctantly consider offers for the player in January.
Perhaps knowing his countrymen were watching back home, Pavlyuchenko showed he was up for the game early on when he charged at the Rubin defence before firing a 25-yard drive just wide of Sergey Ryzhikov's goal.
Rubin, famed for their Champions League win at Barcelona two years ago, proved more than a match for the hosts in the opening exchanges, however.
Roman Sharonov leapt unchallenged to power a header just wide of Gomes' goal and the Brazil stopper then denied Gokdeniz Karadeniz from eight yards with a brilliant athletic tip-over from Christian Noboa's cross.
Spurs were struggling to get into the game, with Aaron Lennon clearly lacking confidence to take on his man down the right flank.
The home side also lacked urgency at times, but sprung into life when captain Sebastien Bassong stormed forward to find Defoe, who clipped a looping shot just inches wide of the Rubin goal.
Minutes later Nelson Valdez should have put the away side ahead at the other end, but he miscued his effort into Gomes' arms.
Sandro, who missed Sunday's draw at Newcastle with a knee problem, put in a series of crunching tackles to deny Rubin as the match entered a lull.
The home crowd were quiet but they soon woke from their slumber thanks to Pavlyuchenko's opener.
Danny Rose won a free-kick on the edge of the box and, after what seemed like an eternity waiting for the wall to move back 10 yards, Pavlyuchenko confidently strode up to the ball and powered a blistering strike that flew in off the bar.
The 29-year-old celebrated what was his second strike of the season in front of the small pocket of Rubin fans.
Pavlyuchenko almost grabbed his second in the last minute of the first half but Ryzhikov tipped the striker's deflected shot around the post.
Ryzhikov blocked Bassong's header just after the break as Spurs looked to grab a decisive second goal, before Gomes pulled off another athletic stop to deny Alexandre Ryazantsev at the other end.
The former PSV man then raised the tension among home fans by hurtling out of his box to hoof clear a dangerous Rubin ball that drifted over the Tottenham defence.
With an hour gone, Rubin manager Kerban Berdyev brought on former Newcastle and Birmingham man Obafemi Martins for Alan Kasaev.
Nelson Valdez then pinched the ball off Danny Rose on the edge of the Spurs box and squared to Noboa but his deflected shot crept just wide.
Spurs continued to be forced onto the back foot and Ryazantsev found Oleg Kuzmin inside the box, but Lennon put in a brilliant well-timed challenge just as the full-back was about to shoot from 10 yards.
The Russians were looking the more likely of the two teams to score and Ryazantsev drew another save from Gomes with 20 minutes left.
Ryzhikov then pulled off a good save to deny Defoe after Lennon had beat his marker to whip in a good delivery from the right flank.
Sensing that Tottenham were looking vulnerable, Redknapp brought on Younes Kaboul for Sandro and also introduced Luka Modric for Lennon.
Rubin continued to dominate the game and the quiet 24,058 crowd inside White Hart Lane became nervous as the game entered its final 10 minutes.
Sloppy defending allowed Martins into the box, but Kaboul came to the rescue with a crucial block to deflect the Nigerian's shot wide.
Valdez then headed wide from eight yards from the resulting corner.
Rose thought he should have had a penalty with when he was brought down in the Rubin box during a rare Spurs attack, but the referee waved play on.
The home crowd had to endure three nervous injury-time minutes, but Tottenham held on for the win.