Harper, who led the Atlantic Coast Con-ference last season in passing efficiency, completed 13 of 18 passes for 142 yards while playing just the first half.
Harper's Orange squad defeated the White squad, 16-7, in the annual game that caps spring practice.
The two squads played four 15-minute quarters, but the final 20 minutes were played with a running clock.
Harper hit sophomore Xavier Dye with 8:05 to play in the first quarter on a 20-yard scoring strike. His second TD pass was a 10-yard toss to Tyler Grisham with 12:20 left in the second quarter.
Dye finished the game with six catches for 87 yards to lead the Orange team receivers. Paul Macko was the top rusher with 10 carries for 36 yards. C.J. Spiller had 20 yards on eight carriers and two catches for 12 yards in limited work.
James Davis, the second leading rusher in Clemson history with 3,130 yards, sat out the game after having shoulder surgery last week and wide receiver Jacoby Ford is recovering from a broken ankle suffered at Maryland last year. Both are expected to be ready to play by August.
The Orange defense held the White to negative 9 yards rushing and forced three turnovers.