Reading pulled one back through substitute Hal Robson-Kanu in the final moments and were denied a penalty deep in injury-time.
Newly-promoted Reading had only seven shots on goal - five of them with the game effectively dead - compared with the visitors' 23 and remain winless in three league games this season.
Reading however opted to change their man between the sticks, with struggling Adam Federici dropped altogether and youth product Alex McCarthy making his Premier League debut.
Villas-Boas seemed to have instructed his side to test the 22-year-old McCarthy as several players tried their luck early on.
McCarthy rose to the challenge in the fifth minute in parrying away a Gylfi Sigurdsson header from a Bale free-kick, then palming a powerful Jan Vertonghen follow-up wide of the near post.
Spurs were dominating possession and made it count when Sigurdsson threaded a superb ball down the channel to split Harte from his centre-halves. The advancing Aaron Lennon pulled back for Defoe, who finished low into the far corner with an excellent first-time strike.
Defoe belied his stature in bringing down a long ball over his shoulder to fire just wide on 24 minutes and his side should have been two in front seven minutes afterwards.
The busy McCarthy, yet to put a foot wrong, showed a nervous heavy touch to allow Defoe to nick the ball off his toe and run wide. Sigurdsson arrived for the cut-back and struck his close-range shot firmly, only for Alex Pearce to produce a superb goalline block.
Reading had not been in action for 25 days thanks to their postponed clash at Sunderland and were showing it, with Harte guilty of another poor touch to almost put Defoe and Lennon in behind again. In comparison William Gallas and Vertonghen were superb in defence for Spurs.
The second half brought few clear-cut opportunities but plenty of high-tempo end-to-end action, with Tottenham also patient when necessary with their passing.
Adam Le Fondre, on at the break for Jem Karacan, brought an edge to the Reading attack, with Pavel Pogrebnyak continuing to run himself into the ground for no reward.
As the home side built momentum - without creating chances - the crowd was silenced by a goal of fortune from Bale with 19 minutes remaining.
Walker attacked the byline and pulled back for the Wales star, whose first-time right-footed strike came off his favoured left and spun over the diving and luckless McCarthy and into the far corner.
Three minutes later it was three: the hapless Kaspars Gorkss dallied on halfway and the England striker won the ball from him before racing into the box, backing off the other defenders, and arrowing a finish into the far corner with his left foot.
Clint Dempsey appeared for his Spurs debut but, after Gallas had cleared off the line from Le Fondre, it was another sub who got on the scoresheet to please those fans that had stayed behind.
Noel Hunt, also on as a sub, found Le Fondre and his perfect clipped pass to the far post was turned in by Robson-Kanu.
MAN OF THE MATCH
Jermain Defoe - Who says a little man cannot lead the line? Brilliant brace from the England striker.
READING: McCarthy 6, Gunter 5, Harte 5, Gorkss 5, Pearce 7, Karacan 5, Leigertwood 5, Guthrie 5, McCleary 6, McAnuff 6, Pogrebnyak 5. SUBS: Robson-Kanu 7, Le Fondre 8, Hunt 6.
MATCHCAST: FULL COMMENTARY AND STATS