The sides drew 1-1 in the first leg at Old Trafford, leaving all to play for between the respective German and English champions.
Bastian Schweinsteiger cancelled out Nemanja Vidic's opener last week, but the midfielder is suspended for the return leg along with Javi Martinez.
Guardiola has also been hampered by recent injuries to Thiago Alcantara and Xherdan Shaqiri, further limiting his options for the visit of David Moyes' men.
"We only have 14 first-team players so I haven't got too many options," said the Spaniard.
"We're playing at home. That's an important factor (but) it's never easy against English teams. I think they'll sit very deep.
"They play very defensively and always look to counter - it's something they do very, very well.
"United is a very big team. Before the first game, everybody just was talking about Bayern. But now people know that Manchester can win in Munich.
"But we will play at home, with our fans we can win this game."
Victory at the Allianz Arena would keep Bayern, who retained the Bundesliga last month, on course to secure a treble for the second season in succession.
Guardiola feels the game against United could come down to "small details" but revealed he has not had Bayern practising penalties in case of a shootout.
"If we win, we're through. If not, we're out. It will come down to small details," he added.
"(Penalties are) less about technique and more about courage. It's all in the head.
"In the quarter-finals you never have a second chance. The pressure is high and we always have done well in this situation.
"It is all about small tactical details. Our players know, after the experience in Manchester, how United plays. My players know their strength and weaknesses."
