Having won 2-1 in Cyprus last week, Spurs squandered an early chance to extend their lead when Harry Kane had a penalty saved by substitute Romero Pulpo after first-choice goalkeeper Karim Fegrouch had to be stretchered off following a collision with Kyle Naughton.
However, Kane made amends with a neat finish in the 45th minute and Paulinho made it 2-0 early in the second half, before Andros Townsend did manage to convert a spot-kick on 66 minutes after a handball in the box.
It is fair to say things could not have gone much better for former Argentina international Mauricio Pochettino since swapping Southampton for north London, having not only won all four matches but earned plaudits for the manner in they have secured those results.
The latest victory came at the expense of AEL Limassol, who were no match for a free-flowing Tottenham side who cruised into the Europa League group stage.
The Cypriots were a shadow of the side that threatened to cause a shock last week, when Spurs just managed to eke out a 2-1 comeback win on a bobbly, cut-up pitch in warm conditions.
Tottenham had no such issues with pitch or climate in north London and looked likely to be in for a comfortable evening when Fegrouch brought down Kyle Naughton with just six minutes on the clock.
The AEL goalkeeper was taken to hospital after receiving a nasty-looking knee to the head in the collision, which did not immediately cost his side as replacement Romero denied a poor Kane penalty.
It was a missed opportunity Tottenham never looked like they would pay for, though, and they eventually turned their dominance into the opening goal on the stroke of half-time when sloppy play allowed Kane slot home.
Paulinho provided the assist and was the benefactor of more sloppy play from Cypriots minutes into the second half, firing low across the goalkeeper.
Townsend then celebrated his England recall by slotting home from the spot midway through the second half, securing a comfortable win and Spurs' place in Friday's group stage draw.