The Brazil forward was preparing with his teammates for their El Clasico friendly against Real Madrid tomorrow night. But he was left fuming as he left the session prematurely.
The duo appeared to come to blows after they challenged for the ball and then squared up to each other before being separated by team-mates.
The 25-year-old had to be physically restrained and was held back by Sergio Busquets before throwing his vest to the ground.
Neymar stormed away and let his frustration show as he kicked a ball in anger as he left the field.
Semedo only joined the club two-weeks ago from Benfica for £26.8million and can be seen walking away as the rest of the Barcelona players restore order.
The Portuguese star was strongly linked with a summer move to Manchester United but oped to join the Spanish giants.
The incident comes amid reports that Neymar has been given the green light to leave the Catalan giants for Paris.
But Marca report club president Josep Maria Bartomeu has suggested it ultimately comes down to the players to decide as and when they move on.
Speaking to the New York Times, Bartomeu said: “Neymar is one of our best players and we do not want to lose him.
“We want him to continue with us, he still has four years left, but the players decide if they want to go so there’s nothing more to say.
“We need him because, if we want to win [trophies], we need to have the best players.”
Neymar has reportedly pulled out of a promotional event in Shanghai. His involvement in a transfer was cited as the reason.
Neymar’s team-mate Ivan Rakitic has urged him to snub a £197m move to PSG.
The Croatian star is keen to see the Brazilian star stay at the Nou Camp as the Spanish giants bid to reclaim La Liga supremacy after finishing runners-up to arch-rivals Real Madrid last season.
Speaking in Miami, the 29-year-old midfielder warned the attacker would not be revered in France the way he is in Spain.
He said: “We want to do important things this season and he is a key piece.
“Footballers like Ney are not everywhere, not just as a player, but as a person. He knows he’s very important for us.
“We already know what we think. The team is like a family and we all want him to stay. Whatever he decides, you have to respect it 100 per cent.
“But as a companion and great friend, I tell him to stay with us. The affection he has here, he will not find anywhere.
“I hope he stays with us.”