Salzburg were on the verge of the Europa League's last 32 after snatching a dramatic 1-0 victory over Levski Sofia.
Franz Schiemer's header four minutes into injury time gave the visitors all three points to put them six points clear at the top of Group G.
However, Villarreal's victory over Lazio means they still need one more point to be sure of progression.
It was Salzburg who started the brighter, with barely a minute on the clock when Marc Janko gave Georgi Petkov his first test of the night with a shot from the edge of the area.
Petkov then punched clear Dusan Svento's close-range effort.
At the other end, Hristo Yovov had a good sight of goal but saw the danger cleared by Ibrahim Sekagya, before Cedric Bardon blazed over.
Salzburg goalkeeper Eddie Gustafsson punched cleared from Georgi Sarmov, and then held a shot from Darko Tasevski.
The chances continued to come in the second half, which began with Schiemer heading just over the Levski goal from close range.
At the other end, Petkov parried clear Svento's shot and then held on to an effort from Tasevski.
Janko sent a free-kick over the bar, but it was Levski who continued to enjoy the edge, with Tasevski testing Gustafsson once again.
Lachezar Baltanov had a good sight of goal from Youssef Rabeh's free-kick, but sent his effort wide.
Salzburg then enjoyed a good spell, started when Sekagya headed narrowly wide in the 74th minute.
Christoph Leitgeb then sent a free-kick just over, before Petkov saved from Schiemer.
But despite all the chances at both ends, the game was seemingly drifting towards a goalless draw.
Two minutes into injury time, Leitgeb had one more effort on goal, but could not come up with a shot to trouble Petkov from the edge of the area.
But just when it seemed each side would finish with a point, Salzburg struck.
Schwegler crossed from the left by-line for Schiemer to finish with a header to the bottom left corner of the net.
