Andre Villas-Boas' team had their chances but went down to goals either side of half-time.
Spurs had the first chance after 10 minutes but Gylfi Sigurdsson saw his shot blocked and four minutes later Aaron Lennon was denied twice when Diego Alves saved his shot and then got up to block the winger's second attempt.
Lennon had another effort blocked before the visitors were punished for not taking their chances when Jonas fired into the top corner from 25 yards with 18 minutes gone.
Goalkeeper Brad Friedel kept his side in the game three minutes before half-time when he saved at the feet of Feghouli before clearing the loose ball.
Valencia increased their lead with 14 minutes remaining, though, when Feghouli shot across Friedel and into the far corner.
Andros Townsend had a stoppage-time shot saved by Alves as Spurs tried in vain to grab a consolation.