Dutch side PSV Eindhoven also qualified for the last 16 but 2004 champions Porto were eliminated together with Slovakian newcomers Artmedia Bratislava and Germany's Schalke 04.
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So tight was Group E, however, that a 3-3 draw would have meant Schalke went through at the Italian club's expense and there were ugly scenes at the final whistle with punches thrown in scuffles among the players.
PSV, who lost in last year's semi-finals to Milan, leapfrogged Schalke to finish second with their 2-0 home win over Fenerbahce. Peru's Jefferson Farfan made one and scored one for the Dutch side.
AC Milan finished with 11 points, one clear of PSV, with Schalke, on eight points, forced to settle for a place in the UEFA Cup.
Rangers became the first Scottish side to make the Champions League knockout phase and in doing so may have saved manager Alex McLeish's job after a 1-1 draw with Group H winners Inter Milan.
Amid frenzied scenes in Glasgow, Danish forward Peter Lovenkrands cancelled out Adriano's early header for Inter, who also had midfielder Cristiano Zanetti sent off.
The Scottish champions then had to wait for an agonising few minutes for the result from the Artmedia-Porto game to come through.
The 0-0 draw at a mud-bound Bratislava ground meant Rangers finished second on seven points, one clear of Artmedia who claimed the UEFA Cup place at Porto's expense.
The qualification issues in Groups F and G had already been resolved and Olympiakos Piraeus and Anderlecht took advantage to record notable wins.
Brazilian former Barcelona striker Rivaldo scored Olympiakos' late winner in a surprise 2-1 home victory over nine-times former champions Real Madrid, who had already qualified from Group F and whose caretaker coach Juan Ramon Lopez Caro fielded a second string team.
ANDERLECHT SURPRISE
Unbeaten French side Olympique Lyon confirmed their status as group winners with a 2-1 win over Rosenborg Trondheim thanks to stoppage-time strike from another Brazilian, Fred.
Rosenborg were already assured of the UEFA Cup place.
Holders Liverpool won Group G after a 0-0 draw at fellow English qualifiers Chelsea and Anderlecht ended their dismal run with a 1-0 victory at Real Betis, who had already secured the UEFA Cup place.
Anderlecht's win ended their record run of 12 successive Champions League defeats and defender Vincent Kompany's goal was their first in the group.
On Wednesday, the remaining three places in the last 16 will be resolved with much attention focused on Manchester United's trip to Benfica.
The draw for the knockout phase takes place on December 16 with the first legs due to be played on Feb. 21 and the second legs on March 8.
