The attacker was pleased to have a chance to impact on the game despite not being the starting XI in the 2-0 victory at Arsenal on Wednesday
Both sides missed penalties in the first half, with Mesut Ozil and David Alaba the guilty parties, while Gunners' keeper Wojciech Szcezny was sent off for bringing down Robben for the Bavarians' spot-kick.
Toni Kroos eventually broke the deadlock with a stunning curling effort from the edge of the box early in the second period and Muller then came off the bench to score a killer second and put his side firmly in control of the last 16 tie Champions League tie ahead of the second leg in Munich.
"I was not surprised at not starting," the Germany international, 24, told Sky. "Pep and I talk to each other so I knew what was coming.
"Of course I am not happy with it. But he knows and is aware that I am a total team player. A match lasts longer than 60 minutes and I am happy I could come in and help the team."
The Bavarians will host Arsene Wenger's men at the Allianz Arena on March 11 in the return leg.