Jones and Evans have missed United's last three games with their respective hip and calf injuries.
Winger Nani, who has been out for two and a half months with a hamstring injury, also sat out training at the AON Training Complex in Carrington.
Striker Danny Welbeck, out for over three weeks with a knee problem, took part in training though, as did full-back Rafael, who has been missing since he suffered concussion against Arsenal 12 days ago.
Club-record signing Juan Mata did not train as he is cup-tied.
United are favourites to come away from Tuesday's last-16 first leg in Athens with a win.
Olympiacos are unbeaten at the top of the Greek Super League, but they are down to just two fit strikers following a thigh injury to top scorer Javier Saviola.