Prospect Zach Lee (3-4) had another rough outing for Albuquerque (18-21). The right-hander gave up five runs on eight hits and two walks in four innings of work.
The Isotopes led 1-0 after Clint Robinson's two-out, RBI double in the first inning. The wheels then came off for Lee in the second.
With the bases loaded but two outs, opposing pitcher Billy Buckner (3-1) singled through the left side to tie the game. Jace Peterson then followed with a two-run single to center that put the Chihuahuas (18-21) ahead for good.
Former Isotope Alex Castellanos would add a two-run double in the third inning to make it 5-1. Adam Moore's solo homer in the fifth accounted for all of El Paso's scoring.
Albuquerque loaded the bases with one out in the ninth. Tim Federowicz scored on a wild pitch and Trayvon Robinson scored on a groundout, but Mike Baxter grounded out to shortstop Tyler Greene to end the game.
Federowicz went 3-for-4 to lead the Isotopes offensively. Veteran Jeff Francouer also went 3-for-4 for the Chihuahuas.
Albuquerque gets an off-day Wednesday before heading for heading for Fresno on Thursday. The Isotopes will send Henry Sosa (1-2, 3.72 ERA) to the mound against the Grizzlies' Mike Kickham (1-3, 3.16).