The Germany international equalised in the closing stages against their 10-man opponents to seal the Bundesliga club's progression to the next round, along with Los Che
The Bundesliga outfit were on top during the early exchanges but they failed to make the most of their dominance. Los Che were reduced to 10 men in the first-half but they showed immense determination to score late on through Sofiane Feghouli.
Mauricio Pellegrino's men had already booked their place in the next round before the game, but Bayern also registered their berth in the last-16 with a late equaliser from Thomas Muller.
Die Roten showed their hand early as they put the Valencia defence under pressure with a high pressing game. The hosts were struggling to get the ball out and they were fortunate that Guaita was on hand to keep out Dante's header in the 18th minute.
However, Jupp Heynckes' side were struggling to get Claudio Pizarro involved and their lack of focus in attack almost cost them just after the half hour mark, but Manuel Neuer saved brilliantly from Feghouli.
It appeared as though that positive momentum instantly evaporated as Antonio Barragan was dismissed for a terribly late tackle on David Alaba, but it actually induced Los Che's best spell of the game.
The hosts kept up their positive, determined attitude and and were by no means making it easy for last year's runners-up. With nine second-half minutes played a cross into the box found Soldado but the Spain international's header flew straight into the arms of the keeper.
Bayern remained unable to make their man advantage count and they were let off the hook when Soldado sprung the offside trap but blazed well over the bar on the hour mark.
Spurred on by the scare, the visitors finally forged a chance of their own as Ribery cut the ball back for Muller. However, the 23-year-old failed to make a decent connection with the ball and Guaita saved with ease.
As Bayern pressed, Valencia's legs began to tire and as a result substitute Mario Mandzukic was the recipient of a free header in the area with 20 minutes remaining. The keeper was helpless as the ball flew through the air but the effort crashed off the outside of the post and went behind.
By the 77th minute it looked to be a disastrous miss. Feghouli won the ball in the opposition half and dribbled his way towards the box. From there he unleashed a shot which took a deflection off Dante and bounced into the net, out of the reach of Neuer.
With nothing to lose, Bayern threw men forward and Mario Gomez made his first contribution on his return to the side by teeing up Muller to fire into the corner, with the ball taking a slight deflection off Feghouli.
The draw means that both sides will be in the hat for the next round, though the group winner will be decided on the final match day.