Barcelona drew 2-2 with Atletico Madrid and remain second in La Liga, one point behind Real Madrid who can go four points clear if they beat Getafe on Wednesday night at the Santiago Bernebeu.
Messi dinked a penalty down the middle just after half-time to reach the milestone at the Camp Nou.
That gave the hosts a 2-1 lead but Atletico hit back. Saul Niguez converted his second penalty of the night in the 61st minute after Nelson Semedo felled Yannick Carrasco.
Atletico stay third, two points ahead of Sevilla, who won 3-0 at Leganes.
Barcelona have drawn three of their five games since Spanish football resumed after a three-month lockdown during the coronavirus pandemic.
Wilting fortunes
The droop has heightened speculation that coach Quique Setien will be replaced for allowing Real Madrid to regain the advantage in the championship.
Setien's judgment was also under the spotlight. He handed a start to 20-year-old Riqui Puig and left the 120 million euro France international Antoine Griezmann on the bench.
"It's true that taking him out of the team like that is hard for a player of his level,” said Setien of Griezmann.
“But the circumstances forced me to do it. I will speak to him, not to apologise but it is a decision he has to understand."
