Videos shared on social media showed supporters of both countries fighting outside Headingley and security personnel being forced to intervene, while ESPNcricinfo reported that at least two fans were evicted from the ground during the match.
The clashes continued after the match ended, with supporters charging on to the pitch and some fans captured on camera throwing punches at each other in the stands. The ICC has promised to take action against any offenders.
"We're here to leave a good impression of my team and also my country. So if you look at my country, there's not good going on in the last 40, 45 years. But we're here to show to the world we want friendship," Naib said.
"To all the audiences watching these kinds of matches, this is only a cricket game. Just watch the cricket game. It's a sport.
"To all audiences who are watching matches, please just watch like a sport."
Naib said that while he understood the emotions in the stands and appreciated the atmosphere in the ground, the fans should have refrained from encroaching on the pitch as soon as the final ball was bowled.
"I love this kind of audience to cause the cheering, both sides," he added. "I think they love the players... so they're really excited to meet them and to hug them.
"But it's not good to come in the ground, to tease the players or tease the groundstaff and other staff... Everyone loves their players, they love their heroes.
"So they don't want to harm anyone. They just want to hug and touch. For me, it's nothing (but) it's not good for them coming on the ground. You can say discipline-wise, it's not feeling good at the end."
As for his team's defeat, Naib pointed to the loss of veteran pace bowler Hamid Hassan with a hamstring injury after his second over as the moment that turned the tide against Afghanistan.
"We had bad luck," he said. "With Hamid Hassan, he's our main bowler. The wicket was really slow. It was not supporting medium pacers like me.
"But the bad luck is that Hamid was unfit, so if he was still in it to the end, maybe it would be really difficult for them. I think the main turning point is Hamid."