The Trojans will play second-ranked Stanford, which defeated UCLA, 4-0.
Both Coach Andy Jackson of Mississippi State (21-7) and Dick Leach of USC (21-3) agreed the Trojans' winning doubles point was the key.
In what turned out to be see-saw match, Mississippi State's Laurent Orsini and Remi Barbarin pushed the Trojans' Lukas Horvorka and Adam Peterson to a tiebreaker before losing, 9-8.
"If there is a turning point, it was in the doubles," Leach said. "We have won 20 of 22 doubles points this year . . . we expect to win that point."
Said Jackson: "I honestly felt the doubles point was very important to us, especially if you're going to upset a team."
USC won or was leading in all six singles matches. "I give credit to USC," Jackson said. "They ran us out of the match in the singles."
In the No. 1 singles, top-seeded Wayne Black of USC beat the second-seeded Orsini, 6-2, in the first set. Orsini was ahead, 5-4, in the second set when the match was suspended.
Black has won nine matches in a row and is 26-4 this season.
Fourth-seeded Seth Denawetz of Kalamazoo College rallied to beat fifth-seeded Tom Reifenheiser of Wesleyan College of Connecticut, 3-6, 6-3, 6-2, in the singles final of the NCAA Division III men's tennis championships at Redlands.