Braga picked up their first victory of the campaign against Partizan Belgrade in the clash between Group H's also-rans as Lima curled a sweet free-kick over the wall and beyond Vladimir Stojkovic's despairing dive, before Matheus added a second at the death.
Marseille got off the mark in Group F as they inflicted a third successive defeat on MSK Zilina as Lucho Gonzalez's corner was headed home by Souleymane Diawara, although Martin Dubravka could have done more to keep it out.
Ajax moved level on four points with AC Milan although they were left hanging on for their 2-1 victory over Auxerre in Amsterdam.
Bayern Munich are in firm control at the summit of Group E but they were given a huge helping hand from CFR Cluj as the Romanian visitors contrived to score two own goals and conceded a 3-2 loss.
The race for second place in Group E is tight after Basel claimed their first victory with a surprise 3-1 success away to Roma.
Alexander Frei's blistering opener was swiftly cancelled out by Marco Borriello's assured finish, only for Samuel Inkoom to again silence the Stadio Olimpico moments before the interval and Adilson Cabral to seal the victory in the closing seconds.