Holders Bayern defeated Arsenal 2-0 at The Emirates while Atletico scraped past AC Milan 1-0 at the San Siro.
Toni Kroos opened the scoring in London for Pep Guardiola's side when he curled a stunning right-foot shot into the top corner in the 54th minute.
Second-half substitute Thomas Mueller headed the second goal for Bayern in the 88th minute following a cross from Philipp Lahm.
An incident-packed first half yielded two missed penalties and a sending-off.
Arsenal playmaker Mesut Ozil's weak spot kick was easily palmed away by Manuel Neuer in the eighth minute and Bayern's David Alaba smacked his penalty against a post after keeper Wojciech Szczesny was dismissed for bringing down Arjen Robben in the area.
At the San Siro, striker Diego Costa secured victory for Atletico when his powerful header nestled in the net with seven minutes to go.
On Tuesday night, Barcelona won 2-0 at Manchester City while Paris St Germain romped to a 4-0 victory at Bayer Leverkusen.
The other four first-leg ties will be staged next week.
(Editing by Tony Jimenez)
