The hosts had to endure an early onslaught from Los Blancos as Jose Mourinho’s men tried to silence the crowd.
Dean Huijsen had the first major chance of the game, but at full stretch, he could only guide a deep cross onto the palms of Alvaro Valles.
The Betis goalkeeper was left helpless minutes later, but his goalpost came to the rescue after some neat interplay around the box involving Kylian Mbappe and Arda Guler, with Vinicius Junior ultimately hitting the upright from a tight angle.
That appeared to be something of a wake-up call for the home side, who subsequently started to show signs of life.
Antony was their brightest spark, winning a series of corners and forcing Thibaut Courtois into a diving save at his near post.
Nevertheless, Betis’ defensive heroics were required again just before the interval, with both Natan and Marc Bartra blocking Mbappe’s efforts on the line after he looked set to score from Vinicius’ selfless pass.
Mbappe went close to breaking the deadlock just after the restart when he whistled a curling effort wide, but the visitors struggled to maintain any pressure.
Betis weren’t causing any danger in attack, but they looked comfortable at the back, leading to a frustrated Mourinho making a triple change just after the hour mark.
Manuel Pellegrini, meanwhile, made changes of his own, and one of them provided the breakthrough with 10 minutes to go. Courtois did well at full stretch when saving Nelson Deossa’s header from a corner, but Parrott reacted quickest to turn the loose ball into the net from close range.
The drama wasn’t over, however, as Carlos Espi’s late equaliser was ruled out by VAR, only for a needlessly clumsy challenge from Natan on Vinicius Junior to concede a penalty deep into injury time.
Mbappe took his time in the run-up, but his poor penalty was saved by Valles to clinch all three points to send Betis joint top of La Liga with both Real Madrid and Barcelona on nine points.
Mourinho, meanwhile, suffers his first defeat in this second spell in charge of Real, which is hardly the best preparation for his team’s UEFA Champions League opener against another of his former teams, Inter Milan.
Flashscore Man of the Match: Alvaro Valles (Real Betis)