Albuquerque (74-67) had just five total hits, including only one extra-base hit, a double by starting pitcher Angel Castro.
Castro (8-5) pitched six effective innings, allowing just two runs on seven hits one walk while striking out four batters.
The Isotopes could not provide any support, however, against Matt Neil (3-3) and three relievers. Neil scattered four hits and one walk while striking out six over six shutout innings.
New Orleans (71-70) jumped ahead in the fourth inning on Rob Brantly's RBI double. Chris Coghlan would add a leadoff home run in the fifth to make it 2-0.
Brantly would add a two-run homer in the eighth and Coghlan would add an RBI single that same inning to put the game out of reach for the Isotopes.
John Baker went 2-for-3 for Albuquerque to pace the otherwise silent lineup.
The Isotopes will continue their season-ending series Saturday at 5 p.m.