This marked a tense European first match for head coach Thomas Frank, whose team battled to hold onto an early lead thanks to a shocking howler.
Tottenham enjoyed a ideal start when a Spurs attacker crossed a grounded ball into the box, which unbelievably rolled into the net after a mishandling by Villarreal's keeper Luiz Júnior.
The visitors fought for an tying goal throughout the match, with Nicolas Pépé showing himself to be a constant threat down the wing.
Refereeing decisions were met with questioning, particularly when the Dutch center-back challenged a Villarreal attacker on the verge of the penalty area late in the second half, but escape with a yellow.
Pépé then curled the resulting free-kick narrowly off target, leaving Spurs to feel a huge sigh of relief.
After the half-time, the home side looked content to defend their one-goal advantage, allowing onslaughts from the visitors.
Changes were made by each managers, with Thomas Partey introduced to boos from the Tottenham fans.
In spite of late efforts, Frank's men stood firm to earn a crucial three points in their Champions League first match.
This turned out to be a match remembered by one error and numerous anxious periods for both clubs.
The victory represents a strong start to Tottenham's Champions League season, even if questions linger about their capacity to compete at this stage.
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