FC Basel were unable to match Lausanne's Dutch exploits, with Christian Gross's men beaten 2-1 at home by Feyenoord. There was disappointment too for St Gallen who left Bruges empty-handed after conceding two second half penalties.
In a fast-paced but scrappy match, Basel did well to come back after Feyenoord's Bonaventure Kalou had put the visitors ahead on the hour with a well-worked goal fired in from near the penalty spot.
The Swiss side needed just three minutes to get themselves back in the match, top-scorer Jean-Michel Tchouga rising unmarked to head a Philippe Cravero cross past Feyenoord's keeper Jurek Dudek.
But just as it appeared that Basel would be heading into the second leg on equal terms, the Dutch side snatched a late winner.
Basel defender Olivier Kreuzer played a short ball out of the area, which Feyernoord striker Paul Bosvelt proceeded to leap upon. The Dutch international skipped along the edge of the area, dodging two defenders in succession, before lifting the ball over the outstretched body of Basel keeper Miroslav König.
Before the match Christian Gross had predicted that his side would need to produce two "extra-special performances" to reach the third round. Now they need to pull out one amazing result in Rotterdam.
St Gallen are also looking at a tough second leg following their defeat in Belgium. Marcel Koller's team appeared to be heading towards an impressive away win when Ghanaian striker Charles Amoah put St Gallen ahead in the 29th minute.
But the Belgian side, who have won all 10 of their domestic league fixtures this season, turned the match around thanks to two penalties.
Shortly after half-time Nzelo Lembi buried a penalty conceded when Marc Zellweger handled on the goal line. With 12 minutes left Zellweger was punished once again, this time for a foul, with Sven Vermant converting the second spot kick.
swissinfo with agencies