The Gators used a 15-0 run late in the second half -- fueled by Prather -- to pull away from the Crimson Tide and remain unbeaten (14-0) at home.
Even though Florida won its 13 Southeastern Conference games by double digits, this one easily could have gone the other way.
"Casey, thank God, gave us good minutes," coach Billy Donovan said. "If he didn't play well, we probably would have had a hard time winning the game."
Erik Murphy led Florida (23-5, 13-3 SEC) with 15 points. Kenny Boynton added 13, and Scottie Wilbekin chipped in 11.
But there's no doubt Prather was the key. He played relentless defense and was equally impressive on the other end. With Prather leading the way, Florida outscored Alabama 23-5 over the final 10 minutes of the game.
"I was definitely trying to bring energy because we looked a little dead offensively and defensively," Prather said.
Trevor Releford led the Tide (19-10, 11-5) with 12 points. Trevor Lacey and Nick Jacobs added 11 points apiece.
Florida made just 2 of 13 shots from 3-point range, but made up for it by making 22 of 26 from the free-throw line.
Alabama was 4 of 10 from the charity stripe.
The Tide really went cold from the field, making just two baskets after taking a 45-37 lead with 12:23 remaining.
"You've got to be able to manufacture some offense," coach Anthony Grant said. "We had opportunities that we let slip away."
Missed shots, bad passes, charges, Alabama did a little bit of everything to give up the lead on the road. It was the complete opposite of what Alabama did right during a 14-4 run that put the Tide ahead.
"Defensively, we weren't as locked in as we during that stretch," Lacey said.
The Gators gladly took advantage en route to clinching a first-round bye in the SEC tournament. Florida can secure the No. 1 seed by winning one of its remaining two games or having Kentucky lose later Saturday.
Donovan cared little about those accomplishments after the game. He was more concerned about his team's problems.
Florida used a 12-0 run to open up a double-digit lead early in the game, making this look like it would be another lopsided affair.
But the Gators stopped making shots and starting giving up baskets at every turn. It was concerning for Donovan because it's the kind of emotional letdown he has tried to rid his team of the last two years.
Instead of moving the ball and getting everyone involved, the Gators started taking ill-advised shots and trying to do too much.
"We've deviated from who we are and we've got to get back to that," Donovan said.
Getting healthy could help.
Bench players Will Yeguete and Michael Frazier II returned from injuries but clearly weren't at full strength. Yeguete missed six games following arthroscopic surgery to remove loose bodies from his right knee, and Frazier sat out Tuesday night's loss at Tennessee because of a concussion. Frazier also missed two days of practice this week with back spasms.
Neither did much against the Tide.
Yeguete missed both shots, had one rebound and one turnover in 11 lackluster minutes. Frazier missed his only shot and had a turnover in 6 minutes.
"I couldn't get anything out of Frazier at all," Donovan said. "And Yeguete tells me after the game that he was absolutely petrified going out there."
Prather picked up the slack, a welcome sight for Florida since he's been banged up all season. He missed several games because of a concussion and a few more with a high-ankle sprain.
He banged his head against the Volunteers, needed stiches above his left eye and created concern about another concussion. He passed all his baseline tests, though, and turned in one of his best performances in three years.
"I thought we were a little drained," Donovan said. "I thought Casey, for whatever really, was really focused and locked in. ... Scottie wasn't himself. I didn't think Kenny Boynton was himself. Patric (Young) wasn't himself. Murphy looked a step slow. It was just one of those games where you sometimes can't maybe put your finger on it.
"I was really, really, really disappointed in my team. Disappointed in my team that I didn't do a better job getting them ready to play and I couldn't have been any prouder the last 9 minutes."