The showdown between OL Reign and Gotham FC was highly anticipated as an emotional farewell for the 2019 Ballon d'Or winner and her former US women's national teammate Ali Krieger.
But the retirement party came to an abrupt end as Rapinoe went down in the third minute with a non-contact injury, grasping at her right calf before limping off the field as fans at San Diego's Snapdragon Stadium gave her a standing ovation.
"The worst possible outcome," Rapinoe told reporters after the match.
"Obviously, devastating to go out of the final so early."
Rapinoe said she was relying on her trademark sense of humour to overcome the disappointment, as she believes she tore her Achilles tendon but would await further testing.
"You don't always get to have the perfect ending," she said.
Krieger, a defender for the opposing Gotham FC, ran to her friend and offered Rapinoe an embrace as she exited the pitch.
Gotham went on to beat Reign 2-1 to collect their first championship title.
The Olympic gold medalist was sidelined this year with a calf injury but her quick exit from her final professional match nonetheless left fans and fellow U.S. women's national team veterans stunned.
"Absolutely gutted," retired US great Mia Hamm wrote on the social media platform X, formerly known as Twitter.
Rapinoe, who along with her national teammates suffered a shock early exit from the Women's World Cup this year, said she had an overall sense of "peace" despite the injury that marred her final game.
"It's obviously disappointing to go out like that," she said.
"I feel great about my career. I feel so lucky and so grateful to have played as long as I played."
