The Toreros won 6-4 in the resumption of the game that was suspended in the third inning Friday due to fog.
In the regularly scheduled contest, the Lobos jumped ahead on Alex Real's RBI single in the first inning, followed by Andre Vigil's RBI single in the sixth.
San Diego responded in the bottom of the frame as Kyle Holder hit a leadoff single, went to second when Grant Melker was walked and then to third on a wild pitch before scoring on Louie Lechich's groundout to second base.
UNM clung to that 2-1 lead until the ninth when Andrew Daniel hit a leadoff home run to tie the game and eventually force extra innings.
The Lobos used a little small ball to push ahead the winning run in the 11th inning. Aaron Siple singled, moved to second on a sacrifice bunt, took third on a wild pitch and then scored as Real reached on a fielder's choice grounder to second base.
A.J. Carman then retired three of the four batters he faced in the bottom of the inning on two groundouts and a flyout.
In the resumed game, it was tied 2-2 in the bottom of the third with a runner on second base. Lechich stole third base and then scored on Connor Joe's sacrifice fly to give USD a 3-2 lead.
Josh Goossen-Brown belted a two-run homer in the fourth inning to extend the Toreros' advantage.
Chase Harris brought the Lobos within 5-4 with a two-run double in the seventh, but USD added a run in the eighth and finished off UNM in the ninth.
The Lobos and Toreros will finish the series Sunday at 2 p.m.