Mehmet Topal's brilliant long-range strike nine minutes before the break settled the first leg in favour of the Spaniards at the Britannia Stadium.
Valencia, who sit third in the Primera Division, were already hot favourites to win the tie and Stoke must now claim victory in the Mestalla next week to extend their European adventure.
Pulis said: "We needed a break, we needed to score first and that would have given everybody a lift and kept us going. We had some good opportunities in the first quarter of an hour and it just didn't break for us then they scored a wonder goal.
"It's disappointing because Rory (Delap) or (Marc) Wilson could have got out to the ball a bit quicker but it's a fantastic strike, a goal worthy of winning any game.
"They've got some great quality, they're a Champions League side so for us to give them the game we have, I think we've done smashing."
Stoke began well and Jon Walters screwed a shot wide inside the first minute, which turned out to be probably their best opportunity all night.
Valencia took a while to find their passing game but when they did it proved difficult for the Potters to deal with and Asmir Begovic produced a great save to deny Jonas after a jinking run.
The Spaniards seemed determined to walk the ball into the net so there was a certain irony that their goal came from a thundering 30-yard shot from Topal that left Begovic pawing at thin air.
Peter Crouch fired a volley just over the bar towards the end of the first half but chances were few and far between in the second 45 minutes and it was Valencia who came closest when Sofiane Feghouli's shot hit the post and then Begovic but somehow stayed out.
The match became increasingly niggly towards the end, with Stoke frustrated by perceived time-wasting from their opponents and also furious at two challenges by Tino Costa on Dean Whitehead.
The second in particular angered the midfielder, who was left writhing in agony clutching his leg. Referee Peter Rasmussen did not even award a free-kick and Whitehead, who took out his shinpad to show the damage to the official, was booked for his protests.
He told ESPN: "It was studs-up and he could have broken my leg. If I hadn't had my shinpad on it would have broken my leg."
Pulis believes his club have been harshly dealt with by referees in their last three games, with Robert Huth shown a red card against Sunderland but Fulham's Pavel Pobgrebnyak and Costa tonight escaping without punishment.
The Potters boss said: "Deano's got a hell of a gash on his leg from two challenges by Costa, very poor challenges, and again we're on the wrong end of decisions. They could easily have been red cards.
"The disappointing thing is, a bit like Saturday at Fulham, the referee's ever so close and sees both incidents. For all what they say about us, our lads work hard and have a go, they're very honest lads and those were poor challenges. The lads were upset."
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