Swiatek was on a 21-match winning streak and looked on course to cruise into the last 16 when she claimed the opener, but the Kazakhstan player hit back with a brilliant second set where she broke twice.
Four-time French Open champion Swiatek raced off court before the decider and when she eventually returned faced boos from an impatient crowd.
It seemed to knock the top seed off her stride and Putintseva roared to a 3-6 6-1 6-2 victory on her third match point.
“My tank of really pushing myself to the limits became suddenly, like, empty. I was kind of surprised, but I know what I did wrong after Roland Garros,” Swiatek said.
“I didn’t really rest properly. I’m not going to make this mistake again. After such a tough clay court season, I really must have my recovery.
“Maybe next year I’m going to take a vacation (after French Open) and literally just do nothing.”
While Swiatek has to deal with another Wimbledon where she failed to leave her mark, 30th seed Putintseva toasted a memorable win on grass against one of the best players in the world.
History repeated itself for Moscow-born Putintseva after she dumped out Naomi Osaka in the first round in 2019 when her opponent was world number two.
Putintseva broke Swiatek twice in the third set and admitted her exceptional level may have been inspired by a period of boredom on Court One while she waited for the Polish player to return from a toilet break.
The world number 35 added: “I was a bit, like, not annoyed, but she took a lot of time off the court.
“I don’t know what the rules are. She just went to the toilet break. I don’t know what happened, how many minutes she was taking.
“Honestly at some point I was so bored. I thought she was coming. Then I was like moving, moving, she’s not there. Again moving, she’s not there. I was kind of getting bored.
“Then I was just super excited about the third set, that I was playing so well. I was not rushing on purpose.
“I’m very proud of myself that I stepped in and I did it.”
