Published: 2019-12-02 04:16:33 BdST
The Argentine, playing his 701st game for Barca, settled a pulsating and tense encounter in the 86th minute, galloping down the right wing before cutting inside and playing a one-two with Luis Suarez before guiding the ball into the bottom corner.
It was Messi's first goal against Atletico at the Wanda Metropolitano stadium and gave his side their first win over their rivals at the ground in three attempts after successive draws in the last two seasons.
The strike saw Barca return to the top of the standings with 31 points after 14 games, ahead of Real Madrid on goal difference, while Atletico were left in sixth spot on 25 points, having played one match more than Barca and Real.
Atletico were also fortunate not to have a player sent off when Vitolo slammed into Pique's knee with a fierce challenge a few minutes later after picking up an earlier booking.
Atletico had won only one of their previous six games in all competitions and looked intent on making an early statement as they came out pressing Barca high up the pitch and peppering their box with crosses.
One of those nearly resulted in Junior Firpo deflecting the ball into his own net but it bounced against the far post, while soon after Ter Stegen pulled off a marvellous save by using his body to thwart Mario Hermoso from point-blank range.
Barca, who were missing the suspended Sergio Busquets and injured Ousmane Dembele, could not impose their usual passing game on Atletico although Ivan Rakitic spurned a good chance to put them ahead when he scuffed a shot straight at Jan Oblak.
Roared on by 67,000 vociferous fans, Atletico looked more likely to snatch a winner but yet again Messi proved the difference, scoring for the 30th time against the Madrid club to give his side a hugely significant win.