City's 1-1 draw with Bayern in their quarter-final second leg secured a 4-1 win on aggregate that assured them a semi-final spot in Europe's elite club competition for a third successive season.
They will face Real Madrid in the last four.
Guardiola's side are also in the hunt for the Premier League title, sitting four points behind leaders Arsenal with a game in hand.
"The team is exhausted, so I don't know how we are going to recover to play against Sheffield United because we play on Saturday," Guardiola told BT Sport.
"It's so demanding, so I don't know how we will arrive because now is a tough moment for the game on Saturday."
Guardiola said defender Nathan Ake would undergo tests later on Thursday to check the extent of a suspected hamstring injury after he was taken off in the second half against Bayern.
