Centre-half Evans sustained a back problem while Rafael hurt his ankle during the first half at Craven Cottage but Tom Cleverley, who was also withdrawn at the interval, has recovered from double vision to make the flight to the Basque Country.
"We haven't had a lot of injuries," the manager told a press conference in San Sebastian. "I think it's the best Manchester United have been in that respect for a while. But we did pick up three on Saturday, which is very rare - especially by half-time.
"Two of them haven't travelled - Jonny Evans and Rafael - so they're not with us."
The boss is keen for the Reds to consolidate top spot in Group A with a positive result in Spain, after beating Sociedad 1-0 at Old Trafford last month.
"I feel we're playing better and getting some good results to go with it," added Moyes. "Long may that continue.
"I won't take anything for granted. I have a lot of respect for Sociedad. We have to play well if we're going to get those 10 points, which will get us over the line. We've got ourselves into a good position in the group and we have to try to maintain that.
"I think our experienced players have shown they're used to the Champions League and that's shown in the games. I hope that continues."