Having been afforded an extended Christmas break, the pair returned to the club two days later than the rest of the squad.
Both men were subsequently left on the bench for the start of Barca's La Liga trip to the Anoeta Stadium, and watched on from the touchline as Jordi Alba put the ball in his own net in the second minute.
Defeat ended Barca's 11-match unbeaten run in all competitions, and also meant they missed out on the chance to climb to the top of the table above Real, who had lost 2-1 at Valencia earlier in the day.
When asked about resting Messi and Neymar, the coach replied: "This isn't the time to regret those decisions.
"I look at the season as a whole and I do what's best for the team. I thought that it was best not to risk [them].
"[The own goal was] Real Sociedad's only dangerous chance. We controlled the match, especially in the second half when we got closer to their net.
"We deserved more than that. We were a bit unlucky not to have scored the tying goal. Real Sociedad played a complete match."
