"I was pretty upset," said Carlino, who had more turnovers (three) than points (two) in 11 minutes of action.
And his Cougars looked like they were going to be the victims of an upset at the hands of the Waves, who led by 11 points at halftime.
But Carlino and the rest of his teammates shrugged off the slow start and rallied in the second half.
Carlino drilled a game-winning 3-pointer, while falling down, with 12.1 seconds remaining, just before the shot clock expired.
In the end, Carlino redeemed himself and BYU escaped Firestone Fieldhouse with a 63-61 victory.
"I was like, 'If that goes in, that would be the best thing ever,'" said guard Tyler Haws, who scored a game-high 21 points. "And it did. I was pretty excited. It feels so good to get a close win like that."
With the shot clock winding down, and the play breaking down, Pepperdine collapsed on Cougar guard Anson Winder, who found Carlino near the top of the key.
"Right when it left my hands, I knew it was good," Carlino said of his last shot. "It was just a good play by Anson."
Still, it was a bittersweet night for Carlino.
"I kind of have mixed emotions right now, because I’m disappointed in the way we played most of the game," he said. "But it's good to get out of here with a win."
Even after Carlino's heroics, which gave BYU a four-point lead, 63-59, the game still had some twists and turns left.
On the Waves' ensuing possession, Winder fouled Pepperdine's Jordan Baker on a 3-point attempt with 1.3 seconds left.
"Then we came down and fouled, which was pretty scary," Haws said.
Earlier, Baker had nailed a 3-pointer as the shot clock expired and with 1:09 remaining in the game, as the Waves re-claimed the lead they had enjoyed almost the entire contest.
Baker knocked down the first two free throws to cut the deficit to 63-61. Then the Waves called timeout, planning to miss the third free throw on purpose to have a chance to tie the game and force overtime.
It nearly worked, as Baker's miss was tipped back by Stacy Davis, but the ball caromed off the rim just before time ran out.
"I thought their guy left a little early," Haws said of the final free throw. "The refs aren't going to call something like that. We're just glad we were able to tip that thing around and the time expired."
BYU improved to 17-6 overall and 7-2 in the West Coast Conference. Pepperdine dropped to 10-11 and 2-6.
"It was a hard-fought win," said coach Dave Rose. "Our guys should be really proud and excited that we were able to win the game. Our guys regrouped. We found a way to hang in there. We did a better job in the second half. Pepperdine did a great job of taking us out of stuff early."
The Cougars outscored the Waves, 43-30, in the second half.
"This team just finds ways to win," Haws said. "I'm just proud of the way our guys competed to the very end."
Carlino scored BYU's final five points, including a pair of clutch free throws with 1:03 remaining that lifted the Cougars to a 60-59 edge.
In some ways, it was a similar game to the one earlier this month in Provo. BYU trailed by five at halftime, but stormed back by outscoring Pepperdine, 46-16, in the second half.
Cougar forward Brandon Davies recorded a double-double with 20 points and 12 rebounds. Davies, who received eight stitches after suffering an injury at practice Wednesday, wore a headband over the bandage above his right eyebrow.
Carlino finished with 12 points and four assists.
In the first half, Pepperdine guard Nikolas Skouen, who entered the game averaging seven points per game, skewered BYU, scoring 13 of Pepperdine's first 15 points, including three 3-pointers. At that point, he had outscored BYU's entire team by one.
Davies scored 12 first-half points, hitting 6 of 12 shots from the floor. The rest of the Cougars went 4 for 20.
Rose played a few different lineups in the first half, with starters Carlino and Josh Sharp playing just 11 minutes and five minutes, respectively.
Meanwhile, seldom-used Bronson Kaufusi and Cory Calvert each saw five minutes of action.
At halftime, the Waves held a 31-20 lead. It marked the lowest-scoring half of the season for BYU. The Cougars shot just 31 percent in the first half, including 0 for 9 from 3-point territory.
After a 3-pointer by Skouen early in the second half, Pepperdine seized its largest lead, 34-22. At that point, the Cougars started to come alive, going on an 14-4 run, fueled by two 3-pointers by Haws and one by Winder. Unfortunately for BYU, Davies picked up his third personal foul during that stretch, at the 16:56 mark of the second half.
The Cougars battled back to tie the game a couple of times, and a Haws jumper gave BYU its first lead with a little more than six minutes remaining, 49-48, since it was up 8-7 after a Haws jumper early in the game.
The Cougars host Santa Clara on Saturday.
NOTES: Announced attendance was 1,824. ... Davis scored 17 points for Pepperdine while Baker added 12. Skouen finished with 16 points.