Ullrich, who won the 1997 Tour de France, is already under investigation over an incident in early August.
Quick Step came over the final summit behind Sunweb but, led by big guns Bob Jungels, Yves Lampaert and Niki Terpstra, made the difference on the final descent and flat section to triumph on the 62.8km course.
The five-time Olympic champion cyclist had thought about rowing competitively and competing in the sport at Tokyo Games.
Yates, a former track racer whose road racing talents took him to the brink of victory in this year's Giro d'Italia, all but wrapped up overall victory on Saturday after yet another strong finish on the final mountain stage.
Yates was third on the day behind 20th stage winner Enric Mas and Miguel Angel Lopez.
The Briton came in 5sec behind Pinot while Dutchman Steven Kruijswijk was 13sec adrift.
The 27-year-old was paralysed after colliding at full speed with another cyclist during training on the concrete track of the Cottbus velodrome.
Former individual pursuit specialist Dennis clocked 37min 57sec to win the stage, held on a rolling, 32km course between Santillana del Mar and Torrelavega.
Thomas, 32, was a surprise winner of the Tour this year, with four-time champion Chris Froome finishing in third place.
Quick-Step team's Alaphilippe finished two seconds behind Team Sky's Poels.
Herrada leads Britain's Sean Yates by 1min 42 in the overall standings.
Italy's Sacha Modolo finished second, with New Zealand's Patrick Bevin coming third.
Britain's Simon Yates of Mitchelton retains the overall lead.
Frenchman Rudy Molard, of the Groupama team, held on to the race leader's red jersey after finishing safely among the peloton.
The 31-year-old Lee won the women's keirin and sprint events to finish off a tremendous week at the velodrome in Indonesia's capital, where she was also part of the silver-winning sprint team.