Belgian 47th-ranked Van Uytvanck triumphed 5-7, 6-2, 6-1 for her first-ever win over a top 10 opponent.
Muguruza's defeat leaves just top seed Simona Halep, number seven Karolina Pliskova and 10th seed Madison Keys as the remaining top-ranked contenders after two rounds.
In the men's event, third seed and last year's runner-up Marin Cilic was knocked out by Argentina's Guido Pella.
Fourth seed Alexander Zverev was teetering on the brink of defeat when he trailed Taylor Fritz of the United States by two sets to one when their second round tie was suspended for the night.
Elsewhere, Rafael Nadal overcame two time warnings and Novak Djokovic shrugged off a knee problem to battle into the third round.
"I knew that if I let her play, I would lose so I thought, let's go for it," said 24-year-old Van Uytvanck, who has made the third round for the first time. "I may have looked calm but inside I was dying."
Muguruza admitted it had not been her day.
"She played big, took risks and it worked for her but my level was not where I wanted it to be," said the deposed champion. "It's a little bit sad."
World number one Nadal defeated Mikhail Kukushkin of Kazakhstan 6-4, 6-3, 6-4 and will next face Australian teenager Alex de Minaur.
Djokovic, the three-time champion, needed treatment on his left knee on Court Two but still had too much for Argentina's Horacio Zeballos, winning 6-1, 6-2, 6-3.
Djokovic has now made the third round for 10 consecutive years and will face British 21st seed Kyle Edmund.
Cilic blew a two-set lead in his 3-6, 1-6, 6-4, 7-6 (7/3), 7-5 loss to Argentina's Guido Pella, ranked at 82.
When rain forced the tie to be postponed on Wednesday, Cilic was leading by two sets against an opponent who had never won a match at Wimbledon before this year.
But the Croatian collapsed once the match resumed on Court One on Thursday and Pella took full advantage to set up a third round clash with Mackenzie McDonald of the United States.
"Yesterday he was playing so good, hitting the ball so hard that I couldn't do anything," said Pella. "So the rain helped me a lot. Today I played differently, tried to be more aggressive, he started to feel uncomfortable."
Nadal, the 2008 and 2010 champion, was tested by world number 77 Kukushkin who was made to pay for converting just two of 13 break points.
He was also hit with two time violations — one before the match had even started as he sat courtside.
"I didn't know but I don't see a clock here. I don't see a countdown. It's more difficult for me to understand what's going on," said 11-time French Open champion Nadal, who is chasing an 18th major.
For Djokovic, meanwhile, victory was his 60th at Wimbledon.
He hit 15 aces and 31 winners in a commanding win over 33-year-old Zeballos, who was a top 40 player in 2013 but was playing at Wimbledon ranked a lowly 126.
Former world number one Djokovic shrugged off a knee injury he suffered in the match.
"It's most likely a twitch in the muscle or something like this that has affected the knee a little bit. Hopefully it's nothing that will concern me," said Djokovic.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ