Heynckes awaiting news on Muller injury
Muller came on as a second-half substitute, replacing James Rodriguez, but had to be withdrawn soon after with Heynckes sending Thiago Alcantara on for the Germany star.
Bayern won the game 1-0 courtesy of Corentin Tolisso's goal in the 52nd minute, for which Muller provided the assist.
When asked why he took Muller off, Heynckes told Sky Germany: "He had a cramp. I hope it's only that.
"We have to wait until the check-up tomorrow."
Heynckes admitted Hamburg frustrated his side in the first half, but the game opened up following Gideon Jung's second-half sending off.
"Hamburg were highly motivated," said Heynckes. "In terms of fighting they were amazing.
"We had problems in the first half. We didn't have the high tempo we wanted.
"After the break it was better as we had four clear chances to score."
#Heynckes: "It was better in the second half. We had lots of big chances. If you don't put them away, it's always going to be tight." pic.twitter.com/eDl6p29Sf8— FC Bayern English (@FCBayernEN) October 21, 2017
The victory left Bayern level on points with Bundesliga leaders Borussia Dortmund after they were held to a 2-2 draw by Eintracht Frankfurt, something the defending champions were well aware of before their clash at the Volksparkstadion.
"It was a very important game," said Heynckes. "We knew the result from Dortmund before, but we couldn't bring everything we wanted on the pitch.
"In the end it was a very tight game."
Meanwhile, Hamburg midfielder Jung questioned the referee's decision to show him a straight red card for a challenge on Kingsley Coman.
He told ZDF: "It was not my intention to hurt a player and hurt my team. With a man down, it is hard.
"It can be a card, but I think in the situation and the course of the game, it was not necessary."