The football legend brought up the landmark with a Panenka penalty to put Barca ahead, although Saul Niguez's spot-kick meant the Catalans lost ground in the La Liga title race.
Barcelona boss Quique Setien praised Messi for the achievement and suggested that there is "no ceiling" on what he can achieve.
He said: "I suppose that another 700 goals will not be scored by Leo, but he will continue to score.
"You don't know what the ceiling is for a player of this type."
The result was a major blow to Barcelona's hopes of retaining the league title, as they are now a point behind rivals Real Madrid having played a game more, but Sieten admits that he was happy with his team's efforts against a tough Atletico side.
The 61-year-old coach said: "I'm quite happy with them. It's true that we haven't been able to win, but at times we controlled the game well.
"It's not easy against this team. They're disciplined. I'm quite happy with my players' work.
"I don't feel at all under threat. It's a shame. We're having more and more difficulties. Leaving these points behind means we're moving further away from the title. But we have to keep working and Atletico are a good team."
Midfielder Sergio Busquets admitted that it is "looking difficult" for Barcelona to win the league.
The Spanish international said: "To fight for the title is hard if you keep dropping two points every game. We'll keep fighting until the end - we know it's difficult but we'll try.
"We played better today but it's looking difficult for us."