The victory runs the Mustangs win streak to six in a row with a home game against Clarinda coming Thursday.
St. Joseph (29-10, 18-9 MIAA) totaled just six hits Wednesday, and a pair of them came from Abernathy.
The center fielder started the fourth inning with a double off the left field wall. Joe Koerper followed with a ground ball to short that Tandon Dorn misplayed allowing Abernathy to score.
Koerper continued to wreak havoc for the Diamond Spirit stealing second, then advancing to third as the pick-off throw sailed into center. Nick Sebastian drove Koerper in on the next pitch with a single to left opening up a 2-0 lead.
Abernathy stepped to the plate again in the fifth with a runner on second base, and for the second at-bat in a row, he drilled it off the left field wall. Andrew Standifer scored from second on the two-out double anchoring St. Joe to a 3-0 advantage.
Omaha scored once in the seventh and once in the ninth, but Grant Gavin kept the Diamond Spirit at bay to record his fourth save.
Miles Gully worked six innings for the Mustangs only allowing one run on four hits and three walks. His record improves to 2-2, while his ERA drops to 2.13.
Wednesday's game was just Abernathy's second start since July 4. He had struggled at the plate with only five hits in his previous 33 at-bats dating back to June 25.