Spurs suffered a nightmare start to their first European Cup tie for almost half a century, their unfancied Swiss hosts tearing their hapless defence to shreds in the opening 28 minutes at the Stade de Suisse.
But with their hopes of reaching the lucrative group stage hanging by a thread, Bassong and Pavyluchenko scored two priceless away goals ahead of next Wednesday's second leg at White Hart Lane.
The build-up to kick-off tonight saw the home fans unfurl a banner with cartoons of some of the world's greatest players attending school.
And Spurs were taught a painful lesson as goals from Senad Lulic, Henri Bienvenu and Xavier Hochstrasser had them 3-0 down.
But Bassong scored just before half-time and Pavyluchenko struck late on to spare the visitors' blushes somewhat.
Every one of Harry Redknapp's four changes from Saturday's Barclays Premier League opener against Manchester City backfired in the first half, with Pavyluchenko, Giovani dos Santos, Wilson Palacios and Bassong all well off the pace.
The visitors had been heavy favourites to progress over two legs, though Young Boys' shock win at Fenerbahce in the last round meant they were not to be underestimated.
And they immediately proved as much during a frantic opening in which Tottenham were all at sea.
Lulic struck the post in the second minute, Benoit Assou-Ekotto was booked in the fourth, and Young Boys were ahead seconds later.
Thierry Doubai's long-range shot hit the back of Ammar Jemal and fell kindly for Lulic to sidefoot home.
Dos Santos would have equalised three minutes later but for a sprawling save from Marco Wolfli, while Jermain Defoe fired over left-footed from 20 yards.
But Spurs' shocking defending continued and they were 2-0 down in the 13th minute when stand-in captain Michael Dawson slipped near the halfway line, allowing Bienvenu a clear run on goal and which ended with a neat finish.
Defoe somehow failed to connect with a wonderful Pavyluchenko cross, before Spurs conceded a third in the 28th minute.
The visitors were undone by a simple sliderule pass from Moreno Costanzo and Hochstrasser made no mistake to blast the ball over the onrushing Gomes.
Jemal went close to making it 4-0 with a free-kick over the bar before Redknapp responded to the malaise nine minutes before half-time by withdrawing Assou-Ekotto for Huddlestone.
Tottenham desperately needed to score and Bassong came up trumps three minutes from half-time, his towering header from Gareth Bale's corner beating boyhood Spurs fan Scott Sutter on the line.
Defoe also went close with a header as Spurs ended the half on top.
Redknapp threw on Niko Kranjcar for Luka Modric during the break and Spurs certainly made a better start to the second half than they had the first. Pavyluchenko dwelt on Kranjcar's inside pass 12 yards out, then poked Bale's wicked cross over the bar from half the distance.
Pavyluchenko fired over from 25 yards in the 65th minute, moments before Young Boys brought on Christian Schneuwly for Costanzo and Redknapp made his final change, Robbie Keane replacing Defoe.
Bassong was booked for dissent after Bale was harshly adjudged to have fouled Schneuwly and Bienvenu almost rubbed salt into the wound when he nodded over the resulting free-kick.
Bienvenu then became the first Young Boys player cautioned after cynically hauling back Kranjcar.
The hosts were now looking to hit Spurs on the break and almost did so to devastating effect 12 minutes from time when Schneuwly's first-time shot whistled over the bar.
Pavyluchenko and Bassong both went close with headers before Gomes went AWOL, allowing Bienvenu to set up Schneuwly for a close-range volley he blazed over.
It proved costly for the hosts as Pavyluchenko finally came good seven minutes from time to get Tottenham well and truly back into the tie.
The Russian dummied Vedran Corluka's ball and Keane picked out his resulting run, from which he lashed the ball past Wolfli at the near post.
Young Boys made a stoppage-time change when Mario Raimondi replaced David Degen before the final whistle ended a thrilling contest.