The Bayern Munich attacker played a key part in the first goal by playing a clever one-two with Toni Kroos, who then went on to place the ball past Schalke goalkeeper Lars Unnerstall.
Muller then scored himself by shaking off two Royal Blues defenders and proceeding to hit a neat shot into the far corner.
"I feel good physically. Anyone who has seen the game also knows that I do not always score. But I have a clear head at the moment and can quickly [get] rid of any negativity," said Muller after the game.
"For example, I started the second half with plenty of the ball, and I thank my teammates for threading through the right passes."
Bayern Munich play against Wolfsburg next at the Allianz Arena on Tuesday.