"I'm obviously a little bit disappointed with the outcome," Stenson told reporters after finishing one stroke behind American Every.
"I'm as much disappointed with the PGA Tour officials for putting up on the clock on 15 and starting to chase us down the stretch."
Under competition rules, a group is put "on the clock" if it falls behind the allotted time for each hole and has also fallen well behind the preceding group.
Players are then timed on every shot and if they take too long they receive a one-stroke penalty for the second bad time, though not the first.
Stenson did not think it necessary to be put on the clock in the first place, even though his pairing, according to the tour, was the slowest group on the course.
"I didn't see the reason for that really," he said.
"I didn't even read my putt more than just one quick look on 15, three-putted from long range, and then Morgan got a bad time on 16 on his second shot so I kind of rushed my putt from the back fringe and hit that one too hard.
"It's just hard when you don't feel like you can't take the time you want to take. Playing on the clock on 15 and 16 surely didn't help the cause."
Tour rules official Steve Rintoul said officials could not be lenient simply if players were in contention.
"Their 3:56 (three hours, 56 minutes) was the slowest group of the day," Rintoul told Reuters.
"Slow groups get timed, first off or last off."
Stenson's mood was unlikely to have been helped by his third near-miss in as many weeks, having finished fourth in his previous two events.
(Reporting by Andrew Both in Cary, North Carolina; Editing by Ian Ransom)
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