Ruben Castro also missed a last-minute penalty in Monday night's clash at Estadio Manuel Ruiz de Lopera.
The game ended at 2-1 after Betis had held the lead following Lorenzo Reyes' 25-yard curling strike in the 30th minute.
The struggling home side, who are rooted to the bottom of the overall standings and started the game eight points adrift of safety, looked to set to claim three crucial points in their bid to survive until Malaga striker Juanmi netted an equaliser in the 83rd minute.
With a point still something of a positive result for a team which has taken seven of their 22 points from the last four games, they were to be denied even that thanks to Sergi Darder's 86th-minute winner.
The result leaves Betis eight adrift of Osasuna, Almeria and Real Valladolid and nine beind Getafe in a congested bottom section of the table.
Malaga, on the other hand, climbed further clear of the drop zone and into 12th place.
The game had started off fairly evenly until Reyes broke the deadlock on the half hour mark when he curled a strike into the top corner of Willy Caballero's goal.
Malaga struggled to get any shots on target in the first period, and they left it late to hit their straps, with Nordin Amrabat setting up Juanmi for his close range leveller with seven minutes left on the clock.
Amrabat was the provider again three minutes later, with Darder the recipient, as Malaga claimed the winner from the boot of the Spaniard.
Betis had the chance to claim a point from the penalty spot in the dying moments after Nacho Camacho brought down Alfred N'Diaye, but Castro's power-kick hit the crossbar.