The 48-year-old German, who won her first Olympic title in Barcelona back in 1992, scored 90.657 percent at the Accor Hotels Arena to add to her 1992, 2007 and 2017 World Cup titles.
Also seven-times world champion, Werth beat American Laura Graves, on Verdades, by 1.575 percentage points.
Another German, Jessica von Bredow-Werndl, finished a distant third with 83.725 per cent, riding Unee BB.
"It was a fantastic performance from us. She was focused, she was really with me," Werth said of her 13-year-old mare.
"It was one of her best freestyle, if not the best."
World number one Werth, who had won four of nine events going into the World Cup dressage final, made uncharacteristic mistakes in Friday’s Grand Prix as she was beaten by Graves, but there was no repeat of those in Saturday’s decisive Grand Prix Freestyle.
"A lot of people think it is easy to win but you have to listen to the horse. Yesterday was not our day but today we improved. It was a great show," said Werth, the most decorated dressage rider in the event's history.
A bouncy piaffe, near-perfect tempo changes and a lot of power made the difference and six of the seven judges put her first.
The event is part of a joint-final with the World Cup jumping final, which will be held on Sunday.
(Reporting by Julien Pretot,; Editing by Neville Dalton)
