The two centre-backs leave manager Erik ten Hag with a problem to solve, though Maguire - who picked up his injury while on international duty with England - has recently lost his starting sport.
Varane limped out of the 6-3 hammering in the Manchester derby after taking a blow to his ankle in the first half and was replaced by Victor Lindelof, who will deputise tonight alongside Lisandro Martinez.
Aaron Wan-Bissaka and Donny van de Beek remain unavailable, with Ten Hag saying he could not provide a prognosis on the pair.
“They’re not available for tomorrow,” Ten Hag said on Wednesday. “In the case of Rapha, I have good hope (he will be available soon). Harry will take a little bit longer and the other two I cannot give a prognosis.”
Ronaldo starts along with Casemiro in Cyprus, though the returning Anthony Martial is on the bench. Phil Jones, Axel Tuanzebe and Brandon Williams are long-term absentees.
Manchester United starting XI: De Gea, Dalot, Malacia, Lindelof, Martinez, Casemiro, Eriksen, Fernandes, Antony, Sancho, Ronaldo
Subs: Dubravka, Heaton, Shaw, Fred, McTominay, Pellistri, Iqbal, Elanga, Garnacho, Martial, Rashford