The holders claimed a 1-0 win over Viktoria Plzen that extended their unbeaten run and sealed qualification for the last 16.
Neuer admitted that while Bayern were far from their best, his teammates were proud of what they had achieved.
"Matching Barcelona's record is great for us but we were really hoping for a better performance today," UEFA.com quotes him as saying.
"We didn't start well. In the first ten minutes Plzen had two corners and we could not get our rhythm going. Against teams like this it is important to use the full width of the pitch and circulate the ball well."
Bayern are top of their Champions League group with 12 points from their first four games.