However, it was forced to play without the talismanic James for two thirds of the contest, after the Bayern Munich playmaker was replaced by Luis Muriel.
A calf injury meant James was forced to start on the bench in the opening game against Japan, but he returned to the first XI against Poland last time out and put in a sparkling display, setting up two goals in a resounding 3-0 success.
He cut a disconsolate figure as he trudged from the Samara turf, though, heading straight down the tunnel before Yerry Mina's second-half header sealed qualification and sent Senegal out.
"What I can say is I'm extremely concerned, it's a very tough situation for my team," Pekerman said. "I didn't want to address this in comments because it seems one of these topics [that] can overshadow everything else.
"In the last Poland match James felt fatigue but it was only fatigue and that was due to him not being present in the previous match.
"He trained normally for us until yesterday, he stayed on afterwards practicing finishing, free-kicks, penalties. He was fully fit in training and in the last training session there was no hint of any injury but right now I don't know where he stands, to be honest."
Pekerman was asked if the issue was a recurrence of James' calf injury, but the veteran coach was unable to provide a definitive diagnosis so soon after full-time.
"At the moment I don't have that information, I cannot confirm or deny anything, we'll have to wait and see," he said.
"We do hope that we'll hear good news after he's gone for his check-up and we'll get a clear idea of what happened.
"What we're trying to do now is think about what we need to do going forward."