Jackson recorded a career-high 12 strikeouts over eight shutout innings, and the D-backs defeated the Marlins, 5-1, at Sun Life Stadium.
Until Cody Ross's two-out RBI single in the ninth inning off Aaron Heilman, the Marlins were on the verge of being shut out for the first time this season. Jorge Cantu, who doubled, scored the only run.
"He was good," Marlins manager Fredi Gonzalez said of Jackson. "He mixed his pitches well. He kept us off balance. He threw a good game."
The loss snapped Florida's season-best, four-game winning streak. In their three previous wins against the Mets, the Marlins scored 24 runs.
It was a different story on Monday as Jackson (2-5) beat the Marlins for the first time in his career. The right-hander traditionally has had his troubles with Florida, reflected by his 0-3 mark and 11.48 ERA against it entering the game.
The loss also featured All-Star Hanley Ramirez being pulled after the second inning for disciplinary reasons.
Ramirez, who took a foul ball off his left ankle in the first inning, remained in the game for another inning, but wasn't giving the effort Gonzalez expected.
"We expect an effort from 25 guys on this team, when that doesn't happen, we've got to do something," Gonzalez said.
The manager didn't rule out sitting Ramirez on Tuesday afternoon in the two-game series finale.
Without Ramirez in the middle of the lineup, Jackson kept the Marlins in check. Brian Barden, who replaced Ramirez, has been hampered by a sore ankle, but he played the rest of the game, striking out twice in three at-bats.
Jackson scattered four hits, with two by Chris Coghlan, who added a double. His previous season-high for strikeouts was eight, in his last start, against the Dodgers.
"His slider got better as the game went along," Coghlan said. "He was throwing mid-90s, and his slider was working well. I think he was a little erratic earlier in the game, and sometimes, we may have helped him out. At the end, he was throwing everything for strikes, and getting ahead early."
Chris Volstad (3-4) gave up four runs (two earned) in five innings. In six of his first seven starts, the right-hander had worked at least six innings.
Jackson held the Marlins without a hit until Ross opened the fifth with a single to center.
The Marlins had a chance to get on the board in the sixth inning, when the score was 4-0. Coghlan singled and stole second. With two outs, Cantu had an infield single that was off the glove of Tony Abreu, who reached for the ball at third. Not seeing the ball bobbled, Coghlan rounded third hard and headed for home. Instead of attempting to get Cantu at first, Abreu threw home, and Coghlan was out.
"I kept running because I was thinking if Jorge can beat the throw, I can score," Coghlan said. "It was one of those instinctive plays. I didn't see him bobble the ball. I didn't know."
Third-base coach Joe Espada was signaling for Coghlan to stay, but it was too late.
"At the time, I couldn't stop," Coghlan said. "It's one of those instinctive plays. Hindsight is 20/20. Looking back, it's not a play you want to do at 4-0. It was a mistake on my part."
Ramirez was removed just prior to the third inning. In his first at-bat, he fouled the ball off his left ankle area, and he was observed by Gonzalez and assistant trainer Mike Kozak.
Walking it off, Ramirez tapped into a 6-4-3 double play on the next pitch, and he ran slowly to first.
In the field, Ramirez was charged with an error on a play where he was slowed chasing the ball. With two on and no outs, Abreu lifted a soft pop to short left field that landed just out of Ramirez's reach.
Coghlan charged in from left field as Ramirez was going out. Ramirez accidentally booted the ball into the left-field corner, and he was slow chasing it. Abreu reached third as two runners scored. The ruling was a single and an error. Abreu scored on John Hester's single. Two of the three runs in the inning were earned.
"It was self-explanatory," Coghlan said of the bloop hit. "He blooped it in there, and Hanley was trying to handle it. It ended up hitting off his knee, or he kicked it. It was just a play. The ball went pretty far, and they were able to score."
Rain delayed the start 32 minutes, and when play began, the D-backs struck quickly. Conor Jackson doubled and scored on Stephen Drew's RBI single to center.
In defeat, the Marlins had several standout defensive plays. Ross robbed Drew of extra bases with a diving catch in right field in the fifth inning. In the third inning, center fielder Cameron Maybin made a diving grab near the wall, also taking extra bases away from Drew.
"They felt I had settled in and was throwing the ball well the last three innings," Volstad said. "I fell into a groove, and was starting to make some better pitches. Some great defensive plays, too."
Joe Frisaro is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.