Thunderstorms caused a four hour delay to the start of play in threesomes off two tees and conditions were wet throughout the day.
But the wait did no harm to Spieth, who shot a boogey-free seven-under round of 63 which was crowned with an eagle on the par-5 16th where he brilliantly chipped in from 49 feet.
South Korea's Tom Kim was a stroke behind, dropping out of a share of the lead with a bogey at his 16th hole, the par-four seventh - where he was in the rough off the tee.
Argentine Emiliano Grillo and American Collin Morikawa were both on five-under, two shots behind Spieth.
Three-time major winner Spieth, the world number 12 who has yet to win this year, said the wet course was playing long.
"The pivotal holes where you get wedge in your hand, if you hit a nice drive, you're looking to attack. I did hit the fairways on those holes, and that was important. Then the really hard ones, you're just trying to get it on the surface and tap in for par," he said after tying his lowest round of the season.
Spieth has missed the cut in two of his last three starts in a season that has yet to take off.
World number one Scottie Scheffler and number two Rory McIlroy both shot three-under scores of 67 to sit four strokes off the lead.
McIlroy made eagle on the 16th with a superb approach shot from 205 yards settling just inches from the hole but felt he could have gone lower.
"I don't know if I can remember a round where I've driven it that well, at least in recent memory. I drove it really well today and gave myself so many looks from the fairway," he said.
"Sort of walking off the course disappointed with 3-under. I felt on another day when I had have been on song a little bit more, especially with the putter, it could have been a 63 or a 64.
"It was a slow start, and then the eagle on 16 sort of got me going. I played solid. I just feel like I left a few out there," he added.
Disappointing Rahm round
Scheffler, who was playing with McIlroy and Masters winner Jon Rahm and starting on the back nine, bounced back from a double bogey on the 14th where he found the water off the tee.
Spaniard Rahm had a disappointing round, carding a three-over 73 with a double bogey on the 18th, his ninth hole, where he drove into the water.
Lucas Glover, winner of last week's Wyndham Championship, continued his positive form with a four-under 66 and said he felt high in confidence.
"A hundred percent, of course...I feel pretty good about it.
"I played pretty much exactly how I played last week, just didn't make as many putts," he said.
Kim, coming back from an ankle injury, caused a stir online with his choice of three quarter length white trousers.
The South Korean said he was simply trying to avoid getting his pants wet from the drenched grass.
"A lot of people seemed to have a lot of laughs on it, but I just thought it was pretty convenient," he said.
"I chose the wrong color, obviously, for the day, but my caddie Joe actually said he doesn't really care what I do as long as I make birdies and eagles, so it kind of worked," he added after making seven birdies and a bogey.
