Within a five-minute span between the third and fourth quarters, Howard threw a 20-yard touchdown pass to Korey Robertson and a 48-yard TD strike to Quez Watkins. Smith capped the rally with his scoring run as Southern Miss (3-2, 1-1 Conference USA) took a 28-13 lead.
Dalton Sturm threw a 24-yard touchdown pass to Marquez McNair to pull UTSA to 31-29 with 48 seconds left, but the 2-point conversion failed.
Howard was 15 of 20 for 212 yards passing. Smith ran for 178 yards on 17 carries.
Sturm threw for 367 yards and three touchdowns to lead UTSA (3-1, 0-1). Greg Campbell Jr. had 10 receptions for 108 yards, and Josh Stewart made five catches for 101 yards.