Borussia Moenchengladbach midfielder Florian Neuhaus gave the Germans a second-half lead in Innsbruck.
RB Leipzig forward Yussuf Poulsen equalised for Denmark after a superb pass from Inter Milan playmaker Christian Eriksen.
Hummels’ return helped tighten the German defence which had leaked 18 goals in their previous 11 internationals, but the Dortmund defender was unable to stop Poulsen equalising.
“It was a mixed team performance,” said head coach Joachim Loew.
“We defended well, better than in previous matches, but we made life difficult for ourselves.
“It was a little bit of carelessness that led to Denmark’s goal.”
In the build-up, Danish coach Kasper Hjulmand claimed Germany have the “potential” to win this year’s European Championship.
However this was a solid, rather than spectacular display by the Germans, who play world champions France in Munich on June 15, then face holders Portugal four days later in Group F.
The Germans were without a quartet of Premier League stars.
Chelsea’s Kai Havertz, Timo Werner and Antonio Ruediger, as well as Manchester City midfielder Ilkay Gundogan, were rested after Saturday’s Champions League final.
Germany had the best chance of a goalless first half when Bayern Munich winger Serge Gnabry hit the crossbar with a long-range shot a minute before the interval.
Mueller was at the heart of the move which put the Germans ahead just after the break when Atalanta left-back Robin Gosens whipped in a cross which Neuhaus stabbed home.
Denmark needed more than an hour to create a shot on goal, but Eriksen made it count with a magnificent pass to split the German defence.
Poulsen sprinted onto the ball in the area and evaded Hummels’ lunging tackle to fire the equaliser past Manuel Neuer on 71 minutes.
The Germans hit the woodwork for the second time when Joshua Kimmich went close with 13 minutes left.
The Danes had a late appeal for a penalty turned down when Poulsen’s replacement Mikkel Damsgaard went down in the area.
Despite having last played international football in November 2018, both Mueller and Hummels looked assured.
Hummels was solid at the heart of a three-man defence with Mueller leading the attack alongside Bayern team-mates Leroy Sane and Gnabry.
“We were quite strong in attack, but in the end the result is frustrating. We hit the woodwork twice and could have had a bit more luck,” said Mueller.
Loew had made the decision to drop Mueller and Hummels from the national side in March 2019, following the team’s group stage exit at the World Cup in Russia.
Loew, who steps down later this summer after 15 years in charge, has recalled the experienced pair for Euro 2020.
Germany play a final pre-tournament friendly against Latvia on Monday.
Denmark have a final friendly against Bosnia and Herzegovina on Sunday before their opening Euro 2020 game against Finland on June 12.
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