Jakob Jantscher's 19th-minute penalty paved the way for a spectacular comeback by Salzburg who clinched a place in the knockout stages of the Europa League at the expense of Paris St Germain.
The Austrians needed to at least match PSG's result away to Slovan Bratislava, but all seemed lost when a pair of Milos Lacny goals inside the first six minutes in Slovakia left them reeling.
Jantscher's spot-kick gave Ricardo Moniz's men hope and Brazilian Leonardo struck the equaliser five minutes later. A 52nd-minute own goal from Marian Had completed Salzburg's comeback.
PSG had given themselves the best possible chance of sneaking second place after they also came from behind to claim an exciting 4-2 win over Athletic Bilbao, who were already confirmed as Group F winners.
Jon Aurtenetxe's early goal for Athletic was quickly cancelled out by Javier Pastore and Mathieu Bodmer, and despite a leveller from David Lopez, the French side secured victory late on with an Inigo Perez own goal and a penalty from Guillaume Hoarau.
Lazio beat Group D winners Sporting Lisbon 2-0 in Rome but were left to anxiously await news from Switzerland before confirming their place in the knockout stages behind the Portuguese side.
Victory for Romanian minnows Vaslui at FC Zurich would have taken them through at the Italians' expense, but they fell 2-0 to second-half goals from Xavier Margairaz and Oliver Buff for the already-eliminated Swiss side.
That left the way clear for Lazio to wrap up a relatively straightforward 2-0 win over Sporting at the Stadio Olimpico. Libor Kozak scored just before half-time and Giuseppe Sculli added the second early in the second half.
Besiktas came from behind at half-time to pip 10-man Stoke 3-1 in Istanbul and secure first place in Group E with Tony Pulis' men forced to accept qualification as runners-up.
Stoke led through Ricardo Fuller's 29th-minute strike, but Matthew Upson's 57th minute red card changed the game with Manuel Fernandes equalising from the spot before further strikes from Mustafa Pektemek and Edu.
Besiktas' recovery shattered Dynamo Kiev's faint hopes and the Ukrainians finished with nine men as they ended their campaign with a 3-3 home draw against Maccabi Tel Aviv.
Dynamo led 2-0 through a Shiran Yeini own goal and Oleg Gusev, but the Israelis hit back to lead after the Ukrainians had Leandro and Evgen Khacheridi sent off. Gusev's second salvaged a point for the home side.
Martin Jol's Fulham were left stunned by Djiby Fall's equaliser deep into added time which knocked the Londoners out of the Europa League and handed Wisla Krakow an unexpected lifeline.
Goals from Clint Dempsey and Kerim Frei had Fulham cruising to the win they needed to secure qualification inside the first half-hour against already-eliminated Danes Odense.
But the visitors reduced the deficit through Hans Henrik Andreasen and grabbed a 2-2 draw with the last move of the match when Fall headed home a cross from the right by Espen Ruud.
Fall's goal proved enough for Wisla, whose 2-1 win over Group K winners FC Twente shunted them up to second. Lukas Gargula opened the scoring and after Luuk de Jong's stunning overhead kick equaliser, Tzvetan Genkov grabbed the crucial winner for the Poles.
A late brace from Stefan Nikolic helped former European champions Steaua Bucharest snatch second place in Group J after Maccabi Haifa were beaten by group winners Schalke.
The Israelis started the night knowing victory would be enough to take them into the knockout stages, but Ciprian Marica, Andreas Wiegel and a Jurica Buljat own goal gave Schalke a 3-0 win and left Steaua and AEK Larnaca to play off for qualification.
The Romanians kept their nerve to claim a 3-1 win. Raul Rusescu's penalty opener was cancelled out by Gorka Pintado on the hour, but Nikolic struck in the 70th and 85th minutes to seal victory for the home side.
In Group L, Anderlecht rounded off a 100% group stage record with a 5-3 win over Lokomotiv Moscow, who had also already done enough to guarantee the runners-up spot.
Sacha Kljestan, Fernando Canesin, Marcin Wasilewski, Matias Suarez and Guillaume Gillet got on the scoresheet for the Belgians, while Dmitri Sychev scored twice for Lokomotiv, who had Andrey Ivanov sent off late on.
Also in Group L, already-eliminated AEK Athens earned their first points of the group stage with a 3-1 win over Sturm Graz in Austria. Kostas Manolas, Nathan Burns and Viktor Klonaridis scored for the Greeks.