Hughes' clutch display at the plate allowed Colby Oller to collect his first win of the season as Southeastern earned a four-game split with the two-day series with the Javelinas.
Oller went the distance allowing three earned runs on five hits while striking out five and walking three.
Hughes laced a run-scoring single to center field to plate Aaron Upshaw in the second inning before lining a two-run single to right field to chase in Upshaw and Randall Clay.
The Savage Storm spoiled an exceptional performance by Texas A&M-Kingsville starter Chris Stage, who allowed one earned run on six hits while striking out eight and walking one in seven innings of work.
Southeastern Oklahoma State (2-2) will face Southern Arkansas in its home opener on Tuesday.
First pitch for the doubleheader is set for 1 p.m. at the Ballpark in Durant.