Frenchman Ribery gave the German hosts a third-minute lead after a defensive blunder and Mario Gomez added his 14th goal in his last 11 Champions League games, tapping in from close range to go top of the scorers' list with six this season.
Jonathan de Guzman scored only the second goal of the competition for Villarreal when he cut the deficit in the 50th minute but Ribery made sure of victory with a solo effort 19 minutes later.
"It was very important to secure top spot in the group early," coach Jupp Heynckes told reporters. "I did not like the goal we conceded and that meant we had to up the pressure again."
"We are proud and happy to have reached our goal with a game to spare," Gomez told reporters. "As for Franck, he was outstanding today."
Carlos Marchena's disastrous pass forward only found Bayern's Toni Kroos who picked out Frenchman Ribery in the box for a simple chip over keeper Diego Lopez in the third minute.
Kroos was imperious in midfield, changing pace and direction, as the Bundesliga leaders Bayern laughed off Saturday's defeat to champions Borussia Dortmund as well as the absence of the injured Bastian Schweinsteiger.
"It was a respectable game and my team should emerge stronger," said Villarreal coach Juan Carlos Garrido. "It was a game where things were done well but the result did not reflect it."
