Feyenoord got the win they needed, a 3-1 home success over Wisla Krakow in Group E which ended the Polish side's interest in the tournament.
Ajax sealed the runners-up spot in Group F with a comfortable 3-0 victory at Belgium's Zulte-Waregem, who were already through.
Paris St Germain found some respite from their troubles, with experienced Portugal striker Pauleta and Ivorian Bonaventure Kalou scoring twice in a 4-0 drubbing of Panathinaikos to seal passage from Group G.
Hapoel Tel Aviv, Fenerbahce and Celta Vigo also booked their places in the knockout stage, leaving five more spots to be decided from the final round of matches in Groups A-D on Thursday.
Any nerves Feyenoord had before the start of their clash with Wisla at De Kuip were quickly settled when Nicky Hofs headed in but the Poles were soon level through Pawel Brozek's finish after Jakub Blaszczykowski's spectacular run.
Jonathan de Guzman restored Feyenoord's lead four minutes before the interval from Joonas Kolkka's cross. Midway through the second half Greek striker Angelos Charisteas made it 3-1 and Wisla's misery was complete when Dariusz Dudka was sent off.
"I'm pleased with this win, we are not always the most stable team but we won again," said Feyenoord coach Erwin Koeman.
Top spot in Group E went to Blackburn Rovers after Lucas Neill fired in a stoppage-time winner to defeat runners-up AS Nancy 1-0 at Ewood Park, guaranteeing a last 32 tie against one of the third-place finishers from another group.
Only by hitting the self-destruct button could four-time European champions Ajax fail to qualify and the 1992 UEFA Cup winners suffered no mishaps, easing past Zulte in Belgium.
Ajax, who had to lose by five goals to miss out, quickly led through Klaas-Jan Huntelaar and the Dutch international grabbed a second goal 12 minutes after the break. Johnny Heitinga hit the third.
Unbeaten Espanyol sealed top spot in Group F and made it four wins out of four, Walter Pandiani netting the only goal at home to eliminated Austria Vienna.
Security was tight at the Parc des Princes with PSG playing at home for the first time since a policeman shot dead a 25-year-old fan and injured another while under attack from supporters after their 4-2 defeat by Hapoel Tel Aviv on November 23.
In a must-win game, PSG made no mistake against Panathinaikos who still finished top of the group.
Pauleta lobbed Pierre Ebede Owono for the opener on 28 minutes and the PSG skipper doubled the lead three minutes into the second half with a low shot from inside the box.
Ivory Coast striker Kalou then netted twice within five minutes to complete the rout. Hapoel also qualified from Group G, getting the point they needed in a 1-1 draw at home to Mlada Boleslav.
Fenerbahce appeared on their way out of the tournament after two goals from Japanese striker Naohiro Takahara handed Eintracht Frankfurt a 2-0 lead after 52 minutes at the Sukru Saracoglu in Istanbul.
But the hosts stormed back with goals from Tuncay Sanli and Semih Senturk, the equaliser coming seven minutes from time. Celta Vigo also went through from Group H after drawing 1-1 at Palermo.