Sevilla were on level terms and looked to be growing as an attacking threat in the second half when, in the 66th minute, Mesa was given his marching orders.
The former Swansea City midfielder had been involved in a number of tussles throughout the match, predominantly with Betis midfielder William Carvalho, and a collision with goalkeeper Pau Lopez saw referee Jesus Gil Manzano produce a second yellow card and the subsequent red.
But television replays showed Mesa did little wrong, as Lopez ran towards him with the ball in his hands and proceeded to jump straight into the midfielder, even catching him on the back of the head with an elbow.
Sevilla players and coach Pablo Machin were astonished as the red card was held aloft, with some arguing that Gil Manzano would have actually awarded the visitors a penalty had he made the right decision.
The RFEF Competition Committee's appraisal of the situation read: "When viewing the images, it is observed that the cautioned player [Mesa], although moving in the direction of the rival goalkeeper [Lopez], does not do it with such forcefulness as to interpret that he intervenes with [Lopez's] advance.
"On the contrary, it is concluded that the adversary is the goalkeeper, who throws himself over the cautioned player, knocking him down. It is suggested that there is a manifest error reflected in the referee's action."
Betis went on to win the match thanks to an 80th-minute strike from fan favourite Joaquin, but Sevilla will at least be able to count on Mesa again for their next game against Getafe after the international break.