The United States grabbed a dramatic silver when the last rider into the ring, Laura Graves on Verdades, scored the second highest mark of the day behind Werth, bumping Britain into the bronze medal position.
Leading the German charge as usual was the indomitable Werth, who has won a record eight gold medals in dressage events at the WEG.
Werth raised eyebrows with her decision to go with mare Bella Rose, who just recently returned to competition after four years off, over Olympic mount Weihegold or the established Emilio.
But the move proved a stroke of genius as the German scored a personal best of 84.7.
She was joined on the podium by Sonke Rothenberger with the day's third best mark, Jessica von Bredow-Werndl (ninth) and Dorothee Schneider 13th.
Werth, Rothenberger and Schneider were all members of Germany's gold medal-winning team at the Rio Olympics.
Britain's Charlotte Dujardin, who rode the now retired Valegro to gold in the individual event at both the London and Rio Games, also had a new ride teaming up with Mount St. John Freestyle but the fifth best result of the day was not enough to secure the silver for the third consecutive WEG.
The top six nations qualified for Olympic spots. Germany, the United States and Britain were joined by Sweden, Netherlands and Spain.
The dressage competition was run in calm conditions while just 250 miles (402km) east of the Tryon International Equestrian Center Hurricane Florence lashed the Carolina coast with wind and rain, flooding roads and overflowing rivers.
It was an ominous prelude of the damage the huge storm could inflict on Friday when it makes landfall.
The WEG is not expected to be in the direct path of the storm but could still feel a significant impact, with heavy rains forecast to extend into the Appalachian Mountains.
(Editing by Ian Ransom)
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