Senad Lulic, Henri Bienvenu and Xavier Hochstrasser fired Young Boys into a 3-0 lead after 28 minutes on the plastic Stade de Suisse pitch in Berne but Sebastien Bassong replied before half-time and Pavlyuchenko's unstoppable drive after 83 minutes left next Wednesday's second leg in London delicately poised.
In the night's other four ties, four-times European champions Ajax Amsterdam drew 1-1 away to Dynamo Kiev while Norwegians Rosenborg Trondheim beat FC Copenhagen 2-1 at home.
Sparta Prague lost 2-0 at home to Slovakian side Zilina and Zenit St Petersburg eeked out a narrow 1-0 win against French side Auxerre. Five more play-off ties begin on Wednesday including a clash between Werder Bremen and Sampdoria.
Premier League Tottenham have not played in the continent's blue riband club competition since reaching the semi-finals of the old European Cup in 1962 and their hopes of mixing it with the powerhouses of the game in the group stages appeared in tatters as a fired-up Young Boys put them to the sword early on.
However, with two away goals they will now start slight favourites to progress.
"In the end that was a great defeat if there is such a thing because at 3-0 down we were out of it," Tottenham manager Harry Redknapp told Sky Sports.
"We didn't look happy on the (plastic) surface, we couldn't get hold of the ball and we didn't look confident in our play and we were in desperate trouble to be fair. Now the tie is evenly balanced and we have a great chance at home."
Lulic had already struck the post for last season's Swiss runners-up and after four minutes the ball dropped kindly to him on the edge of the Tottenham area and he drilled a shot past Spurs keeper Heurelho Gomes.
Nine minutes later Bienvenu left Tottenham defender Michael Dawson in his wake before calmly side-footing past Gomes. With Spurs in disarray, Hochstrasser rifled a shot past Gomes after a defence-splitting pass by Moreno Costanzo.
The Swiss crowd were in party mood but Bassong silenced them after 42 minutes with a thumping header to give the visitors some hope for the second half.
VERY PROUD
Marco Schneuwly should have restored Young Boys' three-goal lead after the break before Russia striker Pavlyuchenko smashed a shot high past Marco Wolfli after being sent clear by substitute Robbie Keane.
"If someone had told me before the match we would have beaten Tottenham 3-2, I would have been more than satisfied," Young Boys coach Vladimir Petkovic said. "I'm very proud of my team. 3-2 is a very good advantage for the second leg."
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