Rooney is expected to have a pain-killing injection in his injured toe so he can take the field in United's quarter-final second leg at the Allianz Arena.
That will be worrying news for England fans with the World Cup just over two months away.
But Moyes has no qualms about playing the 28-year-old - who had a bad World Cup in 2010 just after suffering an ankle injury against Bayern in the Champions League quarter-finals.
"Everybody knows the character Wayne is and the kind of player he is," the United manager said.
"He is determined to play and if he is determined we would be mad not to [play him.]"
On Friday Moyes revealed Rooney had suffered a toe injury in the 1-1 first leg draw at Old Trafford.
The Scot offered up the idea that the injury could be severe bruising, a hairline fracture or a chipped bone.
Moyes refused to reveal the results of scans on the affected area, but he insists he is not gambling with Rooney's World Cup dreams by playing him versus Bayern.
"We think it's OK," said Moyes, who took his squad to a memorial for the 1958 Munich air disaster on Tuesday.
"We wouldn't do anything medically wrong. We take advice from our doctors and the people who advise us."
Moyes' opposite number Pep Guardiola has been paying no attention to the speculation that Rooney would not start the second leg.
"He will play. I bet you a big glass of beer," said the Bayern boss, who twice beat United in the Champions League final with Barcelona.
United have to score to make it through to the semi-finals, but Guardiola expects Moyes' men to park the bus in Bavaria.
"They are so defensive," the Bayern coach said when asked about his experience of playing English teams.
"They use the counter-attack very well.
"It's always difficult when one team stays there just to defend, and waits until you make a mistake.
"Obviously when they play at home they attack a little bit more but when they play away they defend.
"Maybe Moyes thinks another thing, but I think they are going to wait back with eight or nine players in the box, await our mistake and wait for a free-kick or a corner to punish us."