It was the German club's first UEFA Champions League title and their fourth European Cup overall; Valencia suffered their second consecutive final defeat, having lost to Real Madrid in the previous season.
The knockout phase saw Bayern eliminate the preceding two Champions League winners, Manchester United and Real Madrid, winning all four games in the process.
Valencia, meanwhile, defeated English sides Arsenal and Leeds United in the knockout phase en route to the final.
As a result, La Liga 4th-placed team Zaragoza were demoted to UEFA Cup and their Champions League Third qualifying round spot was vacated.
Deportivo La Coruña, Hamburger SV, Heerenveen, Helsingborgs IF, Leeds United, Lyon and Shakhtar Donetsk made their debut in the group stage.