His nearly 28 1/2-pound second-day sack gave him a margin of more than 7 pounds over his nearest competition, Virginia's Rick Morris and Tennessee's David Walker.
Morris and Walker were tied for second place with 37-10 going into the third day of competition.
Todd Faircloth had a 20-8 day that jumped him from 19th into fourth place. Another big mover, Brent Chapman, went from 15th place to fifth with an 18-13 day and 36-2 after two days.
Lyman's Marty Robinson weighed in 19-09, pushing him to 16th place going into the third day of competition.
Full standings can be seen here.
First prize in the St. Johns Showdown is $100,000 and a qualification for the 2013 Bassmaster Classic. Points earned here count toward a Classic qualification, postseason entry and the Toyota Tundra Bassmaster Angler of the Year award.
Jones, who learned last year how easily a 7-plus-pound lead can evaporate when the game is catching fat spawning bass, is grateful for the three big fish that propelled him into the Day 2 lead. His fortunes were helped by an 8-5, an 8-11 and a 6-something, all taken off beds.
"The big ones are at a premium right now," Jones said. "Three big ones like I caught today are just a blessing; that's the only way I can say it."
He called the 8-5 a "dumb, easy one." That's because before he realized it was there, he almost ran over it, his trolling motor buzzing - something that usually sends a bedding bass for cover. It didn't move. He backed up and flipped once to the fish, and it took his bait.
"I was literally 1 foot from it when I first passed it," he said.
The other two made him sweat for the bites, especially the 8-11. He waited her out and was finally able to catch her.
But the sight bite is tough overall, he said. So tough, in fact, that many pros are backing off a game plan that relies 100 percent on sight fishing, or actually being able to see a bass on the bed and casting to it.
"That's one thing that's helping. You're not having the same pressure in the areas with beds because there just aren't enough fish," he said. "I'm using my time looking for big females - not that I wouldn't spend a cast or two on a pound-and-a-half fish."
Runner-up Morris eliminated sight fishing from his game plan before the tournament began Thursday. He's working bedding areas, but he's casting blind into likely looking grass rather than spending hours trying for one or two giants.
"I have never done well sight fishing in Florida - ever," he said. "Some of my fish are coming off the beds, but I am not seeing the fish and casting to them. I'm just casting all over the place into the vegetation that is everywhere. It's all about the grass on this river."
He said he's covering water with several different baits, changing with the wind direction and speeds, and with sunny or overcast conditions.
"My trolling motor's on high, and I'm a-slinging," Morris added. "My fingers hurt, my wrist hurts, my back hurts."
Other runner-up Walker, who won the final Elite Series event of 2011 in Alabama, was consistent over two days with 20-9 the first day and 17-1 on Friday.
He said the mental game was key - sticking to his plan to sight fish. Unlike Thursday, which featured early catches, Friday's bass came slow and small.
"I just started catching anything I could find at that point," he said. "But late in the day, I ended up catching some of the biggest ones that at first I gave up on today. These spawning fish react much better to the bait later in the day. And you can see better too with the sun up high. Everything is kind of in conjunction."
Day 1 leader J Todd Tucker of Moultrie, Ga., fell to seventh place after failing to find the few kicker bass he needed. His Day 2 bag was 9-9.
Carhartt Big Bass honors of the day went to Faircloth. His 8-15 didn't beat Greg Hackney's 10-9 of Thursday, so Hackney still leads the contest for the Carhartt bonus.