Barcelona's La Liga title hopes faltered after they slipped to a 1-1 draw against Cadiz at Camp Nou on Sunday.
Ronald Koeman's side now find themselves eight points behind league leaders Atletico Madrid who lost on Saturday.
"This hurts a lot because after Atletico's defeat we had the chance to get right back in the race," Barca defender Gerard Pique.
"We had loads of chances, they had hardly any so to concede a late goal like that is difficult to swallow. Given the state of mind we went into the game today, we really had to get the three points."
Messi made his 506th appearance in the league and surpassed club legend Xavi Hernandez's appearance record in the process.
His strike against relegation-threatened Cadiz also extended his La Liga record of scoring against the most different opponents to 38.
The hosts had chances to extend their lead before the break but saw goals from Frenkie de Jong and Pedri ruled out for offside.
Fielding the same starting lineup that had been outclassed 4-1 by Paris St Germain in Tuesday's Champions League round of 16 first leg on Tuesday, a rusty looking Barca failed to build on their lead despite having 81% possession and taking 21 shots at goal.
"I am more disappointed than on Tuesday [after PSG]," Koeman said postmatch. "We could not drop these points. We weren't at our best in attack and we have to defend differently, but I don't like to blame players individually.
"The problem is the lead was too narrow and they could level at any moment, which is what happened. If you don't kill the game, if you don't score the second, they always have a chance to score."