"It's a good hitting team. I knew I had a lead, but I couldn't take anything for granted," said Burnett, who had pitched two complete games before his previous outing. "I kept going after them."
"We had chances. We just couldn't get the big hits," Phillies manager Charlie Manuel said.
Burnett (3-1) allowed two runs and five hits, striking out eight. He left with a 6-2 lead, but the Phillies rallied in the eighth against Florida's bullpen.
Jason Michaels and Jimmy Rollins hit consecutive singles off Jim Mecir to start the inning. Matt Perisho entered and hit Tomas Perez
to load the bases. After Bobby Abreu flied out to shallow center, Thome cut it to 6-4 with a double over Juan Pierre's head in center.
Jones came in and struck out Pat Burrell, intentionally walked Utley and retired David Bell on a shallow fly to center to leave the bases loaded. Jones then put runners on first and third in the ninth before striking out Abreu to end it.
The extent of Mota's injury won't be known until he's examined in Miami on Saturday. The Marlins are also without Antonio Alfonseca, who went on the disabled list last week.
"I hadn't been out there in a situation like that in so long," said Jones, who struggled in a brief stint with the Phillies last year. "I felt the adrenaline rush, but I had to take my time, slow down and make quality pitches."
Randy Wolf (1-3) gave up four runs and eight hits in five innings. He fell to 2-12 with a 5.93 ERA against the Marlins.
Easley, filling in for the injured Luis Castillo, snapped an 0-for-13 slump with a homer in the first, giving the Marlins a 1-0 lead. After Cabrera doubled, Encarnacion sliced an opposite-field shot into the right field seats to make it 3-0.
Cabrera's drive into the second deck in left field put the Marlins ahead 4-0 in the third. Encarnacion had an RBI triple off Geoff Geary in the seventh.
Florida has dominated the Phillies in recent years, winning 27 of the last 37 meetings. In 2003, the Marlins beat out Philadelphia in the final week to win the NL wild-card race and went on to win their second World Series.
Wolf, coming off an injury-plagued year in which he was just 5-8 after an All-Star season in 2003, has allowed 10 runs over nine innings in his last two starts.
"I'm not getting the job done in the first inning," Wolf said. "I'm letting my teammates down. I'm just embarrassing myself out there. I'm making too many mistakes. I'm better than that."
Phillies center fielder Kenny Lofton left the game with acute tendinitis in his right hamstring. Lofton doesn't think the injury
is serious. ... Burnett has allowed two runs in each of his five starts. ... At 10-13, Philadelphia is assured of a losing April for the fourth straight season. ... Thome, who has just one homer this season, struck out his first three at-bats, earning louder boos
after each one.