The Poland international was dropped to the bench on Tuesday as Guardiola opted for Thomas Muller in attack in Bayern's UEFA Champions League trip to Lviv, a move that appeared to backfire as the Bundesliga champion was held to a goalless draw by Shakhtar Donetsk.
Lewandowski has not hit the heights many would have expected this season following his move from Borussia Dortmund, having only scored 11 goals in all competitions.
But Guardiola has no concerns with the 26-year-old's form.
"I am very pleased with Robert," he told reporters. "We have often talked and he knows my opinion on his performance and quality.
"I have no doubts about him."
Guardiola also leapt to the defense of Xabi Alonso ahead of a trip to Paderborn on Saturday, insisting the Spain international is a vital cog for the way he wants Bayern to play.
He added: "We want the ball as long as possible, that's why I want players like Xabi or Thiago [Alcantara]. Alonso was not bought to go behind defenses, but to keep the ball and control [the game].
"When it comes to running behind [opposition defenders], Xabi Alonso is the worst player in the world, but we have not got him for that."