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The Indian duo had finished second best at the Malaysia Super 1000, and India Super 750 this year.
The Spaniard hopes to compete at this year's French Open and the Olympics.
Sindhu pocketed the first game 21-18 and the second game was level 1-1 before the Indian felt discomfort on her left knee.
It turned out to be a forgettable day for the Indian squad as both stars went down in straight games.
The 31-year-old former Wimbledon and French Open champion had been provisionally suspended since October 2022 after testing positive for banned blood-booster roxadustat at the US Open last year
The Serbian defeated Casper Ruud of Norway, 7-6(1) 6-3 7-5 in the final.
The Pole, who had not dropped a set in the tournament, was 4-1 up in the second before Muchova won four games in a row and forced a decider.
He has made it to the French Open final for the second year running.
Alcaraz suffered an injury after levelling the match 1-1 in the semifinals.
The defending champions defeated the Brazilian 6-2, 7-6(7) to set up the title match with Karolina Muchova.