"I had incredible moments. My best wishes to all River fans. I'm leaving on good terms and happy with the way I was treated by fans," he said.
There were also third round wins for Belgian star Elise Mertens, Belarussian veteran Victoria Azarenka and France's Alize Cornet.
She will take on 15th-seeded Maria Sakkari of Greece in the last 16, who stunned Williams at last month's Western & Southern Open.
Pepe has made 99 appearances for Gremio and scored 21 goals since making his professional debut in 2017.
Once again Atletico preferred to play their defensive game and only looked to attack their rivals when they had fallen behind as they were outplayed for long periods.
Havertz, joining his German teammate Timo Werner who arrived at Chelsea earlier this summer, is the Blues' second most expensive signing at 71 million pounds (94 million U.S. dollars).
Patrick Bezerra equalized eight minutes later with a header following Thiago Galhardo's cross.
The women's long jump event saw teenager Qin Huiling better her PB by three times to land the victory at 6.37m. Zeng Rui also renewed her life-time best to win the women's triple jump title at 14.10m, while Fang Yaoqing won the men's triple jump at 16.88m. Enditem
In the other matches on Monday, Anhui defeated Jiangsu 3-2, while title favorites Qingdao Renzhou and Ruichang Biyuan both extended their winning streak by beating Hunan Hualai 4-1 and Xiamen Tefang 4-1 respectively.
Wu Haodong/Wang Chang overcame Deng Jiaqiang/Wu Tuobin 11-7, 11-6, 8-11, 11-3 to take the first point for Zhejiang in the opening men's doubles, before Lei Lanxi beat Ren Pengbo in the men's singles to tie the match for Shenzhen.
The boycott triggered by bonus payments saw the Union clamp down hard on the dissenting players and coaches which led to the dismissal of Simiyu, a former national captain of the sevens and 15s formats of the game.