Messi curled sweetly into the corner of Jan Oblak's goal from the edge of the penalty box with four minutes remaining for his 11th goal in 10 games.

Marc-Andre ter Stegen had earlier made two magnificent saves to deny Mario Hermoso and Alvaro Morata for Atletico.

Barcelona climb from third to move above Real Madrid on goal difference.

Zinedine Zidane's Real defeated Alaves 2-1 to go top on Saturday, while Sevilla - just one point further back - beat Leganes 1-0 to temporarily take second earlier on Sunday.

It had appeared the visitors would be made to settle for a point at the Wanda Metropolitano in Madrid after centre-back Gerard Pique's header had hit the crossbar and Oblak prevented Ivan Rakitic from finding the breakthrough.

Atletico missed several chances to take the lead themselves, but German international Ter Stegen's incredible reaction saves - first from Hermoso's close-range shot and then Morata's header - kept Diego Simeone's side out.

Messi's late winner from a perfect Luis Suarez perfect lay-off means Atletico have failed to win any of their last 19 league matches against Barcelona, a run stretching back to February 2010.

And while defeat was perhaps harsh on Simeone's side, the 2013-14 champions find themselves six points adrift of the leaders in the Spanish top flight.