Harper's 3-pointer with 59 seconds remaining, his only basket of the game, put Auburn ahead 59-56, and he made the first of two free throws with 46 seconds remaining for a 60-56 lead. His free throw with three seconds left was the final point.
Junior forward Desean Murray had 11 points and seven rebounds and junior guard Bryce Brown had 10 points for the Tigers (26-7), who won their seventh straight opening-round game in the NCAA Tournament in their first appearance since 2003.
Junior forward Jerrell Brantley had 24 points and seven rebounds and sophomore guard Grant Riller had 16 points for the Cougars (26-8), who had won 14 of 15 after coming from 17 points down to win the Colonial Athletic Association postseason tournament to advance.
The Tigers will play Clemson on Sunday in the second round. Auburn had lost four of six since losing starting forward Anfernee McLemore to a season-ending tibia and ankle injury.
Brown and Harper, who combined to average 29.9 points per game this season, had just 16 points but came up big when the Tigers needed it.
Brown's 3-pointer with two minutes remaining gave Auburn a 56-55 lead, and Harper gave the Tigers the lead for good a minute later. The two were 4 of 18 combined from the floor.
Auburn backup freshman guard Davion Mitchell missed two free throws with 10 seconds remaining in a 61-58 game, but Riller was short on a contested trey before Harper was fouled.
Auburn shot only 35.6 percent from the floor and was a dreadful 15-of-32 from the free-throw line, but mitigated that by forcing 21 turnovers, a season-high by College of Charleston. The Cougars had the fourth-fewest turnovers in Division I this season entering the game.
Senior guard Joe Chealey, the Cougars' second leading scorer at 18.3 ppg, had only two points on 1-for-3 shooting before fouling out. Chealey appeared to hurt his left foot on his only basket, a driving layup with 9:09 remaining.
--Field Level Media
Charleston | Auburn | |
Jarrell Brantley 24 | Scoring | Mustapha Heron 16 |
Marquise Pointer 3 | Assists | Jared Harper 2 |
Jarrell Brantley 7 | Rebounds | Chuma Okeke 9 |
Jarrell Brantley 4 | Free Throws Made | Mustapha Heron 4 |
Cameron Johnson 2 | Steals | Jared Harper 2 |
N/A | Blocks | Chuma Okeke 2 |
Team | Points | FG% | 3PM-3PA | FTM-FTA | Assists | Rebounds | Blocks | Steals | Turnovers |
Charleston | 58 | 45.1 | 5-22 | 7-14 | 10 | 36 | 0 | 6 | 21 |
Auburn | 62 | 35.6 | 5-24 | 15-32 | 10 | 33 | 4 | 10 | 12 |