Thomas improved his record to 2-5 and tied his season-high with eight strikeouts.
Salt Lake had lost 14 of its previous 15 games. During the unhappy stretch, opponents averaged nine runs and 12.4 hits.
"We've been struggling lately," Thomas said. "It's not that we're not putting forth the effort or working hard. We've had some close games that haven't gone our way and we've had a lot of players leave. Our team is a little ransacked right now. But we're doing the best we can and every day is another chance to win. That's how we look at it."
The Bees jumped on Albuquerque starter Carlos Frias for four runs in the bottom of the first inning.
Kole Calhoun and Taylor Lindsey singled before J.B. Shuck walked to load the bases. Long followed with a two-run single and Shuck raced home on Roberto Lopez' infield out. Drew Heid made it 4-0 when his double scored Long.
The Isotopes got a run back in the top of the second, but Thomas got out of a potentially big inning.
With the bases loaded and one out, Albuquerque's Carlos Triunfel bounced into a pitch-to-home-to-first double play.
"It helped a lot," Thomas said. "We just had a good inning and, as a pitcher, you want to go out and shut the door. I left some pitches up and got in a little jam, but getting out of there was big for the momentum."
With Thomas on cruise-control, the Bees added to a 5-1 lead in the fifth. After Lindsey and Shuck walked, they ended up at second and third after a wild pitch. Long followed with another two-run single.
Salt Lake 7, Albuquerque 4
O Justin Thomas scatters five hits over six innings and pitches the Bees to a 7-4 win over Albuquerque.
• Matt Long goes 3 for 4 with four RBIs as Salt Lake wins for the second time in 16 games.
Albuquerque player reportedly bites off part of teammate's ear
Los Angeles Dodger prospect Alex Guerrero was injured during an altercation with teammate Miguel Olivo during Tuesday's Salt Lake-Albuquerque game at Smith's Ballpark.
Guerrero is a Cuban infielder who signed with the Dodgers last winter for $28 million.
According to a report by Jon Morosi of Fox Sports and the Major League Baseball Network, agent Scott Boras said part of Guerrero's ear was "displaced" after he was bitten by Olivo. Police are investigating.
In the eighth inning of the Bees' 7-4 victory, play was stopped briefly when the fight broke out in the Isotopes' dugout.
Guerrero and Olivo had confronted each other an inning earlier during an Albuquerque pitching change. Standing near the mound, Olivo charged Guerrero before teammates stepped between them.
The Dodgers issued a statement saying the organization was investigating the incident.
The Bees and Isotopes play against Wednesday night.