The Lions lost by three wickets with one ball left in the innings to the Titans, who were crowned champions after a bizarre end to the game.
Swanepoel had finished his spell of 10 overs with the ball, taking 3-44, and left the field around the 43rd over. He headed straight for the airport having signed for Worcestershire in the English County season. Their first game is on Friday.
His own teammates believed he was injured, but when it was discovered he was not, the umpires denied the Lions the chance to use a replacement fielder and they finished a tight game with 10 players on the field.
The Lions have launched an investigation into his conduct and could withhold his No-Objection Certificate (NOC), which means he would not be eligible to play in England.
"I am extremely disappointed in Beyers. His actions go completely against the culture and values of the team which we have worked to build for the last six years," Jono Leaf-Wright, the Lions chief executive, told ESPNcricinfo. "He has let the union and the fans down."
The Lions had already lost coach Russell Domingo for the final after he left on Saturday to link up with Hampshire, though his plans were revealed and signed off ahead of time.