Al-Khelaifi cut a frustrated figure post-match after PSG surrendered a 4-0 first-leg lead as the French champions suffered a heartbreaking 6-1 loss in Wednesday's return last-16 fixture.
Barca scored three goals from the 88th minute, including the winning goal in the fifth minute of stoppage time via Sergi Roberto, as the Spanish hosts completed the greatest comeback in Champions League history.
And Al-Khelaifi lamented PSG's performance in the first half, having headed into the interval 2-0 down and out of sorts at Camp Nou.
"Even if we should have had two penalties, we're not looking for excuses. We didn't play in the first half," Al-Khelaifi said. "After winning the first leg 4-0, it's very difficult to accept losing the second 6-1, but we don't have a choice.
"After our first-leg win, the aim of reaching the quarter-finals was legitimate, but we know in football that that doesn't mean anything.
"We tried to do our best. We didn't manage to qualify, but we'll continue. To concede three times in seven minutes when we had been trailing 3-1 after 88 minutes is very hard.
"I haven't spoken to the players yet, it's not the right time. Everyone is annoyed, it's normal. We're going to calm ourselves down."
FULL TIME: Gutted #FCBPSG— PSG English (@PSG_English) March 8, 2017
PSG head coach Unai Emery was equally as glum after the match in Barcelona as he bemoaned a missed opportunity.
Edinson Cavani's goal just past the hour-mark seemingly ended Barca's hopes, with three goals required for the hosts to achieve the impossible and progress to the quarter-finals.
But PSG were left shell-shocked and with plenty to learn in their quest for European glory.
"For everyone at Paris Saint-Germain, the staff, players and fans, it's a bad day. What happened on the pitch is a negative experience," Emery said.
"Individually, we missed out on a good opportunity to grow. We wanted to grow with the game. In the first half, we didn't play with the attitude we had wanted. We wanted to continue like in the first leg. We wanted to sit back and hit them on the counter-attack. After the third goal, the team was better. We wanted to get a better result by scoring a second goal.
"In five minutes, we lost everything. We weren't able to defend. It's an experience. A negative experience, but an experience all the same. I'm learning for the future. It's clear we passed up a good opportunity."