Cody Kessler threw for 247 yards and a touchdown and Silas Redd ran for 140 yards for USC, which has won three of its last four games under interim coach Ed Orgeron. With the victory, the Trojans became bowl eligible.
Oregon State's Sean Mannion threw for 277 yards and a touchdown but also threw three uncharacteristic interceptions in the loss, the second straight for the Beavers after a six-game winning streak.
Mannion, who went into the game leading the nation with an average of 408 yards passing, looked slightly off against the Trojans. He was sacked eight times last weekend in the Beavers' 20-12 loss at home to No. 6 Stanford.
Mannion hit favorite target Brandin Cooks with a 43-yard pass on the opening series and the Beavers were helped by a pass interference call, but Trevor Romaine's 46-yard field goal attempt was blocked.
The Trojans took over on the 29 and, on the first play from scrimmage, Cody Kessler hit Lee with a 71-yard touchdown pass to put USC up 7-0.
Lee, last year's Biletnikoff Award winner as the nation's top receiver, was questionable going into the game because of a left knee injury that has sidelined him for two of the last three games.
The Trojans went up 14-0 on Allen's 9-yard scoring run late in the first quarter.
Oregon State closed the gap with Mannion's 27-yard touchdown pass to Cooks. On the next series, Ryan Murphy intercepted Kessler's pass and ran back 41-yards to even it at 14 with 9:29 to go in the half.
Allen, a sophomore who had scored two touchdowns this season going into the game, put USC back on top with an 18-yard run and the Trojans led 21-14 at halftime.
Southern California opened the second half with Andre Heidari's 34-yard field goal. Oregon State had a chance to pull closer, but Romaine's 26-yard attempt went wide left.
Allen added a 52-yard touchdown run with 3:25 left in the third quarter to give USC a 31-14 lead.
The Trojans were coming off a 19-3 victory over Utah last Saturday.
Already depleted because of NCAA sanctions that have cost the team a significant number of scholarships, the Trojans have been stung this season with numerous injuries that have forced them to shift players and use walk-ons. Right tackle Kevin Graf (ankle), safety Su'a Cravens (groin), linebacker Morgan Breslin (hip), tight end Randall Telfer (knee) and cornerback Anthony Brown (knee) were among the players who did not play.
Oregon State was notably without senior receiver Kevin Cummings, who suffered a wrist injury sometime during the first half of the loss to Stanford and required surgery. It will keep him out the rest of the season but he could be back for a bowl game.
The Beavers are known for their success against some very formidable Trojans teams. In 2008, the Beavers were 26-point underdogs when they knocked off then-No. 1 USC 27-21 on a Thursday night in Corvallis. Two years earlier, Oregon State topped then-No. 3 USC at Reser 33-31.
The two teams hadn't met since 2010, when the Beavers downed then-No. 20 USC in Corvallis. Ryan Katz threw for 154 yards and two touchdowns while Jacquizz Rodgers rushed for 128 yards and another score in the 36-7 victory.
USC's last win in Corvallis was a foggy 28-20 victory in the 2004 season when the Trojans went undefeated and beat Oklahoma in the Orange Bowl for the national championship -- which was later vacated by the NCAA sanctions over improper player benefits.
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