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.
That unfortunate error from the defender proved to be the decisive moment as, despite enjoying more of the ball for the remainder of the match, Barca failed to find an equaliser.
Messi was introduced at half-time, with Neymar brought on shortly before the hour mark, but neither man was able to conjure up a leveller for their team as Sociedad completed a hat-trick of home league wins over Real Madrid, Atletico and Barcelona this season.
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."
