The Swiss side were the night's biggest winners as they netted twice to leave Zenit with a mountain to climb ahead of the return fixture, while Levante and Rubin ended goalless
Fenerbahce drew first blood in their Europa League last-16 tie with Viktoria Plzen as they returned to Turkey with an invaluable 1-0 away win to their name.
The winning goal came on 81 minutes when Gokhan Gonul's cross from the right found Moussa Sow in the box, and despite the striker's original attempt stopped by the goalkeeper, Pierre Webo followed up to secure a vital Turkish win on the road.
The result ends the Czech side's seven-match winning sequence in continental competition at home and their invincible Europa League run in Plzen.
BENFICA 1-0 BORDEAUX
Benfica used home advantage to their credit after they were gifted an own goal in the first half to come away with a 1-0 success at Bordeaux's expense.
Les Girondins were hoping to become the first club to win at the home of the Eagles, but they came undone on just 21 minutes as Rodrigo's piledriver from the edge of the box crashed against the crossbar which the shot-stopper Cedric Carrasso put into his own net.
Bordeaux now go into the second leg of their clash with Benfica still winless on Portuguese shores.
BASEL 2-0 ZENIT
Basel left it late at St-Jakob Park on Thursday to take a 2-0 lead and full control of their tie with Zenit St Petersburg.
The deadlock wasn't broken until 83 minutes as Mohamed Salah's effort was saved by Vyacheslav Malafeev, but Marcelo Diaz popped up in the right place at the right time to sweep home the rebound.
And in the first minute of injury time, Luis Neto was given his marching orders for hauling down Salah in the box, allowing veteran striker Alexander Frei to convert from the penalty spot for a convincing victory.
LEVANTE 0-0 RUBIN
In the only draw of the night, Levante and Rubin Kazan failed to find a route to goal - or the initiative in the round of 16 - at the Ciudad Valencia, but they did share a red card apiece.
Despite their fair share of snapshots, the action did not simmer until 52 minutes when Cristian Ansaldi tangled with Sergio Ballesteros illegally for his second yellow card of the night, putting the Russians a man down in the process.
And just two minutes later, Michel was also headed for an early bath as his lunge on Gokdeniz Karadeniz was considered excessive by the referee to leave the tie finely posed ahead of the return leg in a fortnight.