Defender Greg Halford, making his full debut following a January move from Colchester, was penalised for handball five minutes before half-time - despite the ball hitting his hand at point-blank range.
Robbie Keane's conversion proved to be the only goal of the game as Spurs moved into the top six.
They came out of the traps as quick as they always do at home and laid siege on Reading's goal early on.
Steed Malbranque had their first good chance on three minutes after being teed up by Aaron Lennon and his shot clipped the outside of the near post.
A minute later it was Royals goalkeeper Marcus Hahnemann who came to his side's rescue when he got down low to deny Keane in the six-yard box.
The American keeper was again called into action on 12 minutes when Malbranque put the lethal Dimitar Berbatov through, but Hahnemann was equal to the Bulgarian.
This sparked the Royals into life and almost straight after they had what was their best chance of the game.
Glen Little picked out in-form striker Leroy Lita unmarked in the box, but he mistimed his free header and the ball skewed against the post before being cleared.
It gave the visitors a little more momentum however and they went on to dominate for ten minutes, during which Dave Kitson forced a fine stop out of Paul Robinson following sloppy Spurs defending.
But Martin Jol's men came back to finish the half the strongest and found themselves ahead going into the break.
Malbranque had forced Hahnemann into another good save and defender Nicky Shorey had also denied Keane with a last-ditch tackle before Spurs were awarded their soft penalty.
To make matters worse for Reading when Hahnemann suffered an injury and was replaced at half-time.
Their confidence was shot to bits and they even allowed the ever-dangerous Lennon to go on a 70-yard solo run before firing inches wide on 51 minutes.
Spurs also had refereeing decision go against them when a Jermaine Jenas goal was disallowed for offside after a beautiful set-up by Berbatov.
Reading only threatened once in the second half, when Lita put another free header wide of the post with seven minutes left.