Bastian Schweinsteiger fired the hosts into the lead seven minutes before half-time and Toni Kroos doubled their advantage with a sweet strike from outside the area with 14 minutes remaining.
The visitors had offered very little in an attacking sense but were given hope in stoppage time when Nelson Valdez headed home Jonathan Viera's cross, but within a minute Adil Rami was sent off for bringing down Arjen Robben in the box and despite Diego Alves saving Mario Mandzukic's penalty, there was not time for Valencia to launch another attack.
These two sides last met in the Champions League final of 2001 but whilst Valencia appear miles off repeating that feat, Bayern showed they will again be a strong contender with a composed display.
Kroos was first to go close with an effort from close range that skimmed the bar on four minutes and the German international forced Alves into a flying save with another effort from range midway through the half.
However, the Bundesliga leaders were finding it difficult to find gaps to exploit as Valencia defended in numbers, so it was no surprise when the opener arrived on one of the few occasions Bayern had the opportunity to counter-attack.
The hosts stole the ball in midfield and Franck Ribery squared for Robben who in turn steered the ball into Schweinsteiger, whose shot took a slight deflection off Aly Cissokho on its way into the net.
Alves then produced another wonderful stop to deny a fierce Kroos effort on the hour mark before Sofiane Feghouli had Valencia's best chance to equalise as he broke clear inside the Bayern penalty area but his shot was deflected to safety by Jerome Boateng.
On 76 minutes Kroos finally had the goal his previous efforts deserved as he collected a loose ball 25 yards from goal and dispatched his shot high into the top left-hand corner.
With the game winding down Valdez headed home Viera's corner to half the deficit but Bayern promptly went up the other end and when Rami bundled into the back of Robben he was shown his second yellow of the night by Turkish referee Firat Aydinus.
Alves though kept up his remarkable record of saving penalties as he stopped Mandzukic's weak spot-kick, but Bayern held on.