It was his 20th consecutive round of par or better at the Houston Open, but not quite good enough to match Putnam, a PGA Tour rookie who birdied six of his final seven holes for a 65 that matched the best round of the day.
Putnam, whose brother Michael also plays the PGA Tour, posted a 12-under 132 halfway total, with fellow Americans Mickelson and Austin Cook (65) on 11-under.
Mickelson sounded delighted with his form and position as he prepares for a tilt next week at a fourth Masters title to add to his previous victories at Augusta National in 2004, 2006 and 2010.
"You want to want to experience being in contention and dealing with that as you enter the Masters," the 44-year-old told reporters.
"You don't want to just hope for blind luck ... because the pressure you feel trying to win the Masters is greater than just about anything we have."
Mickelson has won four times on the PGA Tour immediately preceding the Masters, though only once (in 2006) did he also collect a green jacket the following week.
UPTICK IN FORM
His uptick in form, particularly on the greens, comes after he switched last week back to an old putter he used to win the 2005 PGA Championship.
"Before (last week) I spent hours each day on the putting green, getting my putting back to where I wanted, going back over the drills that made me successful," Mickelson said.
"My short game has been sharp this week (and the) putter does feel a lot better but it's felt better for a while."
Leader Putnam was mired in the middle of the field until his late birdie blitz. He has not finished better than 12th in 14 previous starts on tour.
"I caught fire on the back nine," Putnam said. "These greens are so good that if you start seeing the line you can make a lot of putts."
Canadian Graham DeLaet (67) and American Luke Guthrie (68) were two strokes from the lead.
DeLaet missed the cut in his previous three starts due to wayward driving, a flaw he has finally corrected.
"I've just been hitting foul balls with my driver, digging myself in holes I couldn't get out of," he said.
The cut fell at four-under 140 and defending champion Matt Jones of Australia was among those sent packing.
(Reporting by Andrew Both in Cary, North Carolina; Editing by Mark Lamport-Stokes)
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