The victory snapped a franchise-worst 10-game losing streak for Albuquerque (43-40).
Ely (4-4) scattered four singles over seven innings, allowing two walks and striking out one. The defense behind him was nearly flawless, with only one error on the night.
Jose Valdez followed with a scoreless eighth inning and Jon Link came on in the ninth. With one out, Lorenzo Cain singled up the middle, but Link shook it off and struck out Kila Ka'aihue and Manny Pina to earn his eighth save of the season.
The Isotopes loaded the bases in the second inning on two singles and a walk, but Joe Becker grounded out to third base to end the threat. Albuquerque finally broke through in the fifth as Jamie Hoffmann led off with a single up the middle and Russ Mitchell followed with a two-run homer to left field.
Ely's only real jams came in the third and fifth innings. In the third, Pina singled with one out and Jarrod Dyson singled with two outs, but Ely got Johnny Giavotella to ground out to third base.
In the fifth, Ka'aihue drew a one-out walk and Pina reached on an error by third baseman Corey Smith, but Ely induced a popout by Lance Zawadzki and a groundout by Dyson to end the threat.
Jeff Suppan (7-5) took the loss for Omaha (46-38), allowing five total hits and two walks over seven innings.
The Storm Chasers mustered just six singles as a team after outscoring Albuquerque 28-14 in the first three games of the series.
The Isotopes will return home Monday to open a three-game series with Round Rock starting at 7:05 p.m.