Werth, and at her seventh Games, put in a strong performance and scored 79.89% in the dressage team finals, held in the Grand Prix Special format, with Wendy, a black mare she took over only months ago.
World number one and defending Olympic champion Jessica von Bredow-Werndl later sealed the win for Germany who got a total score of 235.79 points, ahead of Denmark with 235.67 and Britain with 232.49.
"It's a super exciting competition. I don't think we've had such a tight fight in a long while and it's great fun," Werth told reporters before she knew her team made it.
Werth has become the most successful German in Olympic history with eight gold and five silver medals. She is also the most decorated rider.
"Hats off to her. I never try and match Isabell. She is the undisputed queen of dressage", said Britain's Carl Hester, one of the last dressage greats of Werth's generation still competing.
The victory brings some relief to Germany, who so far have failed to deliver on expectations in most sports and are 10th in the medals table, as the Olympics head into their second week. Riders have won half of all German gold medals.
Britain's chances took a hit when star rider Charlotte Dujardin was barred from the competition a few days before the Games over a video that showed her hitting a horse, reviving a debate over the sport's ethics and Olympic future.
Speaking to reporters after his ride, veteran Hester said he was "excited and proud" of his pupil Becky Moody, the young rider who stepped in to replace Dujardin and scored a personal best with her 11-year-old stallion Jagerbomb.
Denmark's Cathrine Dufour had the best individual performance with a score 81.2% with MSJ Freestyle, a mare she took over from Dujardin a few years ago.
Speaking to reporters after his ride, veteran Hester said he was "excited and proud" of the good performance from his pupil Becky Moody, the young rider who stepped in to replace Dujardin.
Denmark's Cathrine Dufour had the best individual performance with a score of 81.2% with MSJ Freestyle, a mare she took over from Dujardin a few years ago.
The Danish riders said the tight result, setting their team just 0.12 percentage points behind Germany after three rounds of jury votes, was a testament to how exciting their sport could be rather than a cause of frustration.
"It was mega fun sport today", said Dufour. Her teammate Daniel Bachmann Andersen added: "If you flip the medal the right way, you can see there's some gold in it."
Asked about her ambitions for Sunday's individual finals, held as a freestyle competition, Werth said: "This we will see tomorrow. In any case, I'm looking forward to it."
Germany have won 14 gold medals, or two thirds of all those awarded in the dressage team competitions in the modern Olympics, including each gold since 1984, apart from 2012 when Britain snatched it on home turf.