In Plzen, there was no repeat for Bayern of their 5-0 thumping of the Czech side in Munich a fortnight ago, with Mario Mandzukic netting the only goal of the game with a 65th-minute header to maintain his side's 100 per cent record.
As a result of the victory, Bayern equalled the most consecutive wins ever recorded in the Champions League, with the tally now at nine after winning the trophy last season.
Real Madrid and Paris St Germain both have one foot in the door of the last 16 after they were held to 2-2 and 1-1 draws against Juventus and Anderlecht respectively to end their own hopes of winning every game in the group stages.
At the Juventus Stadium, the Italian side grabbed the lead against Real via a 42nd-minute penalty from Arturo Vidal before Ronaldo and Gareth Bale struck in eight second-half minutes by the hour mark to edge the La Liga side in front.
Fernando Llorentes, however, rescued a point for Juve to leave Real needing only a draw from their remaining two Group B games to guarantee their passage into the knockout phase.
Juve are now bottom, though, with three points after FC Copenhagen pulled off a shock 1-0 home win over Galatasaray, with Daniel Braaten striking the winner after just six minutes.
In Group C, PSG also need only a point from their final two matches, but were forced to come from behind at home to Anderlecht.
Demy de Zeeuw fired the visitors in front in the 68th minute, only for Zlatan Ibrahimovic to haul the hosts level two minutes later.
That was prior to Anderlecht finishing the game with 10 men after Sacha Kljestan was dismissed in the 82nd minute for a second bookable offence.
After two years of failure to qualify for the knockout stages of the Champions League under Roberto Mancini, Manchester City are finally through to the last 16 under Manuel Pellegrini.
Following a 7-0 Barclays Premier League thrashing of Norwich at the Etihad Stadium on Saturday, City were again in the goals on home soil as they recorded a 5-2 victory over CSKA Moscow.
That result, combined with Bayern's success over Viktoria Plzen, means City and the reigning European champions are the two sides to qualify from Group D.
A Sergio Aguero penalty, after David Silva had been fouled by Zoran Tosic, gave City the lead inside three minutes, with the Argentinian doubling his tally for the night in the 20th minute with a right-foot drive for his 13th goal of the season.
Alvaro Negredo then followed up with a hat trick with goals in the 30th, 51st and 90th minutes, with City's march to victory briefly tempered by goals from Seydou Doumbia in the 45th and 71st minutes, the latter from the spot.
In Group A both games finished goalless, leaving Manchester United and Bayer Leverkusen as the teams still favourites to qualify.
Against Real Sociedad, Robin van Persie twice struck the post, including once from the penalty spot, whilst Javier Hernandez also missed an open goal.
United will be without Marouane Fellaini for the next game in Leverkusen on November 27, however, after the midfielder was dismissed for a second bookable offence in the 90th minute.
Shakhtar Donetsk are still in with a chance of finishing in the top two after their 0-0 draw with Leverkusen, a game in which five players were booked.