The Brazilian forward scored four goals at the showpiece before suffering a serious back injury in his nation's quarter-final win over Colombia.
As a result, he viewed Brazil's 7-1 semi-final humiliation against Germany from the sidelines and will play no part in Saturday's third-place play-off against the Netherlands either.
Despite making a big-money move from Santos, Neymar scored just nine La Liga goals for Barcelona last term and is expected to improve this season.
Bartomeu felt Neymar progressed to a new level in Brazil, hailing the 22-year-old – and fellow Barcelona man Lionel Messi – as the two main men of the tournament.
"Until the injury he was having an incredible tournament," Bartomeu told Barcelona's official website.
"Despite his youth, his progress as a footballer and his leadership made a mark on the Brazil team.
"We have been close to him since the injury, the medical services have been in contact with him and his family. It was a nasty shock for all football fans, especially those of Brazil and Barca.
"I hope he gets fit again soon and wish him all the best. He is very young and will have plenty more chances to win things for his country.
"Whatever happens in the final, Messi and Neymar have been the two big stars of this World Cup."
Bartomeu also took the chance to wish Messi and fellow Argentina man Javier Mascherano the best ahead of Sunday's World Cup final against Germany.
"I hope that Leo Messi and Javier Mascherano win the World Cup," he added.
"They deserve this in recognition of their careers. They are two born winners, I hope they enjoy the final and have plenty of good luck.
"I am very happy that he [Messi] is about to play in the final, he wanted it so much. And he has played a direct role in all of his team's victories and has scored some lovely goals.
"Leo has once again shown why he's the best player in the world."
