The world number one, who will take on Dutchwoman Kiki Bertens for a place in Saturday's final, made a mess of numerous routine shots and her opponent took the opening set having made only one unforced error.
The American survived two break points at 4-4 in the second set, which she eventually won when world number 60 Putintseva served a double fault.
The momentum had swung Williams's way and the American crushed Putintseva in the decider, wrapping it up on her fourth match point with an unreturnable serve.
"I didn't think I was going to win that in the second set, a relieved Williams said courtside.
"I did and I'm really excited."
Williams's game was littered with 43 unforced errors, 37 of them coming in the first two sets against a resilient opponent on Court Philippe Chatrier.
While Williams seemed to be snoozing, Putintseva just had to send the ball back and she played neatly to open a 3-1 lead.
The 21-times grand slam champion rallied back but conceded the opening set when her sliced backhand floated into the net.
She moved 4-2 up in the second, but Putintseva found stunning angles to fight back and she found herself leading 40-30 on the American's serve at 4-4.
Williams saved the point at the net and a second one later in that game when Putintseva sent a backhand wide, before bagging seven games in succession.
In a final shudder, the 21-year-old Putintseva, who had never made it past the third round in a grand slam, saved three match points but caved on the fourth.
(Reporting by Julien Pretot, editing by Pritha Sarkar and Clare Lovell)
Share
