The Swede -- who lost to defending champion Matt Every by one stroke -- was ticked off that he and playing partner Morgan Hoffman were subjected to time constraints from the 15th hole onwards because of alleged slow play Sunday.
Under competition rules, players are put on the clock if they have fallen behind the allotted time for each hole and well behind the preceding group of players.
Once the measure is imposed, shots are timed and players given a one-stroke penalty for the second shot -- but not the first -- on which they are found to have taken too long.
Stenson said the decision "got to me, and obviously I was rushing" as he three-putted both that hole and the 16th, opening the door for Floridian Every to seal the title with a round of 66 crowned by a long-range putt on the final green.
Officials at the Bay Hill course said Stenson and Hoffmann's had been the slowest pairing of the day Sunday.
But the frustrated 38-year-old Swede said he "could not see the point" of being put on the clock.
"When someone is sitting there with a stopwatch it affects you a little bit," he explained, accusing officials of "influencing, potentially, the outcome of this tournament towards the end."
"I didn't really have much time to look at my putt [on the 15th] and rushed that one a little bit, the first one, and three-putted," the PGA Tour website quoted him as saying
"Morgan got a bad time on his second shot on 16, and again I kind of rushed my putting on 16 and three-putted that one. That's really what cost me the tournament, those two three-putts on 15 and 16.
"We might have been a couple minutes out, for sure -- but then again it's normally not the quickest when you're playing in the last group.
"[There are] more people, more movement. You have to back off every now and then for some mobile phones and stuff like that."
The PGA Tour was not immediately available for comment about Stenson's remarks.
Stenson told reporters that "it's hard when you don't feel like you can take the time you want," adding that he was "disappointed with the rules official for pushing us up late in the round for no obvious reason."
And he was unimpressed when told that part of the reason for the imposition of the ticking clock could have been a desire to complete play before live TV coverage came to an end at 18.00 local time.
"I thought we were here to play golf, not to finish at 6pm," he snapped.
Meanwhile, a delighted Every was left to reflect on the 17ft birdie putt on the final green that took him to the title.
"You watch tournaments on TV where guys make putts like that to win and everybody goes nuts -- it's cool to close one out like that," he said.