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.
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"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)
