The United and England captain has been relegated to the bench by both this season and has started just one league game since being left out against Leicester at the end of September.
Rooney is one goal short of the 249 career United goals scored by the legendary Bobby Charlton, but with just three goals this season, and only one in the league, the striker might have to wait a while longer to make history.
And although an injury to Mkhitaryan in Sunday's win against Tottenham will keep the Armenian forward out of United's next two games, Mourinho insists Rooney, 31, is just one of five players battling to start at Selhurst Park.
"I knew that was coming," joked Mourinho when asked if Rooney would start.
"Rooney, (Marcus) Rashford, (Jesse) Lingard, Ashley Young, Memphis Depay -- that's a position where we have lots of players so that will not be another problem, to choose a player to play.
"The problem is Mkhitaryan was playing so, so well and now he's not there."
Mourinho paid tribute to his central defensive pairing of Phil Jones and Marcos Rojo, two players whose United careers have been blighted by injuries and inconsistent form.
With that duo impressing and Eric Bailly returning to full fitness, Mourinho is confident about his defensive options.
"I am surprised with Phil because even with me he had this injury which stopped him for a long time," said Mourinho.
"Now he looks fresh and looks sharp and fast. I think he had a big evolution and I think he played already six matches. Six matches, Phil Jones? I don't remember when he did that.
"A little bit like Marcos because Marcos also had lots of problems with injuries and he also looks free of it.
"In a period without Bailly and (Chris) Smalling, when people could be scared, they stepped up and both played so many matches already -- six without defeat, I think -- playing well and solid so I'm really happy for that."
There will be one enforced change in United's defence at Palace as right-back Antonio Valencia is suspended.
That could mean Matteo Darmian moving to right-back and Daley Blind stepping in on the left.
For struggling Palace winger Wilfried Zaha will face his former club convinced he is now proving his critics wrong.
Zaha returned to Selhurst Park after an unsuccessful stint at Old Trafford two years ago and his form this season has prompted Eagles manager Alan Pardew to bemoan the fact Zaha may be lost to England if the player takes up an offer to play for Ivory Coast.
The 24-year-old made the second of his two friendly appearances for England three years ago but has since been overlooked and is still eligible to change the country he represents.
He sparkled in Palace's 3-3 draw at Hull on Saturday when he scored, won a penalty and provided an assist.
"Before I was known as the Wilf that just does tricks," Zaha said.
"On Saturday I managed to add a shot at the end and it was on target as well! I am happy with my progress.
"Everyone talks about my stats so I am just trying to give them a reason not to talk. I just do what I need to do on the pitch and see who laughs last."