The 67-year-old revealed his disappointment at his side's second-half performance, lamenting their sloppiness as they allowed the visitors back into the game
Die Roten dominated the game in the first-half but stepped off the gas after the break and failed to close out the game in their Champions League opener.
Although Toni Kroos added to Bastian Schweinsteiger's earlier strike, Los Che netted a consolation effort in stoppage-time, through Nelson Valdez, to deny the hosts a clean sheet.
"The final stages must be viewed critically. That should not happen to a team like ours, because we have lost concentration," Heynckes is quoted as saying by Kicker.
"It was a game of patience. Valencia played on the counterattack but had virtually no chance to score."
Captain Philipp Lahm also believed that the Bundesliga outfit should have put a bigger gap between them and the opposition, though he was happy enough with the win.
"A win against the closest competitors in our group, that is a good start. We should have made it 2-0 earlier," he said.
New €40m-signing Javi Martinez was awarded with his first start for his new club in the fixture and expressed his delight at the way he has settled into the team.
"Not only with Schweinsteiger has the interplay already worked well, but with the whole team," he enthused.
Bayern travel to Belarus to face BATE, who defeated Lille 3-1 in France, in their next Group F fixture.