The Rays' loss, combined with a win by the first-place Red Sox, pushed the Rays back to 2 1/2 games out in the American League East.
Jackson's fateful pitches were a slider and a changeup. Wes Helms swung at the slider, Mike Jacobs swung at the change and each swing produced a three-run homer.
The Rays right-hander set the table for Helms' home run by walking two of the first three hitters he faced in the second inning. Helms then hit his fourth home run of the season on a 1-2 pitch.
Jeremy Hermida and Jorge Cantu had back-to-back singles with two outs in the fifth to set the table for Jacobs, who hit Jackson's first pitch into the right-field stands, giving him 16 for the season and putting the Marlins up, 6-0.
Despite once again falling prey to his familiar recipe for disappointment, Jackson said he felt no frustration about the situation.
"It's simple facts once you know the chances of people scoring once you walk them," Jackson said. "It's nothing to be frustrated about. You know the situation, and once it happens all you can do is try and get out of it without any damage being done. And tonight, I couldn't do that."
Jackson fell to 2-6 in his last 12 starts, after winning his first two starts of the season. In addition, he has not produced a quality start in his last five outings.
Jackson's recent results are "not an overt concern to me right now," Rays manager Joe Maddon said. "We just have to get him back to where he had been early on and just making better quality pitches -- with all of his pitches. Fastball command first -- that has not been there for him and everything else works off that. So, we just have to get his fastball command back.
"He had a 22-inning scoreless streak earlier this season, and he did have his fastball command. We just have to get that back and work off that."
Rays catcher Dioner Navarro still believes in Jackson.
"He kept the ball down," Navarro said. "He got behind a couple of times, but he battled back. ... We all know what he's capable of doing. He'll go out there next time and go after them."
While Jackson was hurt by the long ball, Rays hitters cooled Tropicana Field with their swings trying to deal with Marlins starter Ricky Nolasco, who struck out a career-high 12 Rays during an 8 2/3-innings outing to collect his seventh win of the season.
"Their guy was really sharp today," Maddon said. "Tremendous command of his breaking ball, that was uncanny, because he spotted his fastball when he wanted to and was able to throw his curveball for a strike as well and kept the ball inside to lefties."
Jason Bartlett and Gabe Gross each had RBI singles and Eric Hinske hit his 12th home run of the season to account for the Rays' runs.
If Jackson and the strikeouts weren't enough to give Maddon a Maalox moment, Cody Ross' two-run triple in the eighth likely tipped the scale.
With two outs in the inning, Ross hit a ball to the gap in right-center field that B.J. Upton and Gross converged on before each pulling away and letting the ball fall between them. A week earlier during a 6-3 loss to the Rangers, a similar scene played out, resulting in Gross being charged with an error.
"It was just both guys calling for the ball simultaneously, that's what I've been told," Maddon said. "That happens. That happened [today] with our bigger crowd -- and that's good, it gets louder and you do make the call and if it's simultaneous, it can mess you up."
The Marlins then added an unearned run in the ninth when Bartlett committed the team's first error -- since Gross's error a week earlier -- and the Marlins went up, 9-2.
Sunday's loss snapped a five-game home winning streak and gave the Rays only their fourth home loss in their last 26 games at Tropicana Field. Despite the loss, the Rays claimed their eighth consecutive series win at home -- the longest such streak in the Major Leagues this season, and they have won 11 of the last 15 series they have played.
Winning the series "is our goal and it's wonderful we're disappointed," Maddon said. "That's something that hasn't happened here in the past. The expectations have been raised. If you won a couple of games, that's OK, if you lost one. But we don't feel that way anymore. It's disappointing to have not won the third one today. And have the momentum play so well pretty much the first two nights and come in here and not play well today, that's disappointing."
Bill Chastain is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.