Ribery, who had been wisely rested for last weekend's Bundesliga win over Mains because of a sore ankle, scored either side of half-time while impressive Austrian full-back David Alaba and Bastian Schweinsteiger also got on the scoresheet.
Victory made it nine points from a possible nine for Bayern, who are three ahead of Manchester City, the English side who beat CSKA Moscow 2-1 earlier on Wednesday.
The win coupled with a sharp first-half performance left coach Pep Guardiola a satisfied man. "I am happy with the performance of the players," said the 42-year-old Spaniard.
"I had said that I wanted a better display in the first half than had been the case last Saturday (a 4-1 win over Mainz with all Bayern's goals in the second period).
"I believe that in the European matches this season, including the Super Cup win over Chelsea, we have played well but in the Bundesliga it has taken us longer to click into gear and perhaps we need more time."
Bayern started brightly and Ribery went close with an effort that was well saved by Pilsen goalkeeper Matus Kozacik. The 29-year-old Kozacik was Pilsen's busiest player, called into action again shortly afterwards as 21-year-old Alaba let fly from the edge of the area.
The Czech 'keeper was fortunate as he failed to catch the ball cleanly but there was no Bayern player in close to take advantage.
However, the pressure finally told in the 24th minute as Arjen Robben went down under a crude challenge by Czech international central defender Roman Hubnik and Ribery made no mistake from the spot.
The hosts should have doubled their lead two minutes later as Mario Mandzukic beat his man only to shoot straight at Kozacik, but he proved more effective as a provider in the 37th minute as his knockdown set up Alaba, who beat a defender and fired home.
Kozacik may have been unable to stop that effort but he pulled off a stunning reflex save from a close-range Robben header shortly before the break to keep the scoreline respectable.
Bayern didn't let up in the second half with Ribery getting his second in stylish fashion in the 61st minute.
Schweinsteiger scored their fourth three minutes later, turning neatly inside the area after receiving a pass from Mario Goetze, who had just come on for Philipp Lahm.
Goetze then tried his own luck only to see his excellent shot denied by the bar, but the youngster was to get a deserved goal in added time.
Goetze, who moved from Bayern's great rivals Borussia Dortmund in the close season, said it had been an effective performance but nobody should jump to conclusions about them being on course to retain the trophy.
"The group stage is very different to the knockout part of the competition," said the 21-year-old. "Thus it is important people don't jump to conclusions about how good we are."