Gotze has only started one Bundesliga match so far this season but scored Bayern's second goal in the 3-0 win over Olympiacos on Wednesday after being named in the starting XI for their opening Champions League Group F fixture.
Guardiola insists he has no doubt over the World Cup-winning midfielder's ability or attitude but says it is hard to find a place in his regular line-up given the form of Robert Lewandowski and Thomas Muller, who scored twice against the Greek champions.
"I love Mario Gotze, he's a top player. He has massive quality and a good attitude," Guardiola said.
"But I have Robert Lewandowski and Thomas Muller. I can understand that he is disappointed, but I'm here to help him."
Gotze himself believes Bayern can be hugely satisfied with their victory, even though they led by a solitary goal until the 89th minute.
"Three points against a good opponent, so we can be really happy," said Gotze. "Muller obviously scored an outstanding goal."
Bayern return to Bundesliga action against Darmstadt on Saturday.