Trouba, Evander Kane and Michael Frolik each had a goal and an assist in the Jets' first home win since Nov. 15. Ondrej Pavelec made 21 saves, helping Winnipeg bounce back from a 4-2 loss at Buffalo on Tuesday.
Florida had won five in a row, including a 4-2 victory at Ottawa on Thursday night.
"The second game in two nights is never easy, so that start was huge for us," Wheeler said.
"I think our group was kind of chomping at the bit to get going again. Any time you have a tough game like we had in Buffalo and then take a couple of days to stew over it, I think you're almost foaming at the mouth to get back out there."
"We all go through it," Florida coach Peter Horachek said. "It was our back-to-back situation getting in at three in the morning but there's no excuses."
"We played back to back and you get in at three in the morning, I think that's pretty logical," Horachek said.
"We thought it was the perfect opportunity for him to come in and steal one for us, him being fresh and focused, and obviously it didn't work out the way we wanted it to."
Winnipeg (16-16-5) came out fast and dominated the opening minutes. But the Panthers got on the board first when Dustin Byfuglien's attempt to raise a clearing pass bounced off Matthias and he snapped one in at 7:45.
Trouba then tied it with his soft tip at 11:06 of the penalty-filled first. It looked as if Markstrom kicked it into his net with his skate as he scrambled to block the puck.
"We tried to take advantage of their travel and their second in two nights," Jets coach Claude Noel said. "I thought there was a lot of emotion in the first period. The second period lulled a bit, I thought we played one of our better third periods."
Winnipeg grabbed control with two goals in a 33-second span late in the first. Enstrom converted a 5-on-3 chance from the slot at 15:24, and Wheeler then scored on the man-advantage when he deflected Zach Bogosian's shot past Markstrom.
It was Bogosian's first game since that last home-ice win Nov. 15. He was out with what is thought to have been a groin injury.
Kane flipped in Frolik's pass to make it 4-1 just 1:03 into the second as the pair grabbed just enough space for a 2-on-1.
Bjugstad then got Florida back into the game with a wrist shot at 5:55 of the second before Frolik restored Winnipeg's three-goal lead when he snapped in Andrew Ladd's rebound.
Winnipeg's Mark Scheifele had two assists to extend his point streak to five games, the longest active streak among NHL rookies. He has collected 12 points over the last 12 games, dating to Nov. 23.