The result extended Sociedad’s unbeaten run to 11 straight league matches, with seven wins and four draws.
Atletico got on the board with goals from Yannick Carrasco and Jo?o Felix, and an own-goal by Betis defender German Pezzella, under heavy rain at the Wanda Metropolitano Stadium.
Betis, which had won five of its last six league matches, stayed a point behind Atletico and has played an extra game.
Carrasco opened the scoring with a shot from inside the area in the 26th minute.
The Madrid club, still in last place, had started with seven straight losses.
Mallorca, winless in four straight matches, had also conceded in stoppage time in a 1-1 home draw against Sevilla and a 2-2 draw at Valencia, when both Valencia’s goals came after the end of regulation.