The 14-year-old, who rode for Reale Avintia Racing, was involved in a crash involving multiple riders on Turn Five.
After receiving treatment on the track, Perez was rushed to hospital by helicopter but died on Monday morning.
“Andreas has not been able to win this race,” said a team statement.
“We have lost a great driver, but above all a great person and we will miss him very much.”
Perez impressed in last year’s European Talent Cup as he claimed two wins and further podium finishes.
He ended 2017 fourth in the rider standings before making the move to the Moto3 Junior World Championship.
“It is with great sadness that we report the passing of Andreas Perez Manresa,” said MotoGP in a statement.
“The incident happened in the second race of the day for the Moto3 category, with the red flag shown immediately. The rider received medical attention at the side of the track before then being transferred to the hospital by helicopter.
“Despite the best efforts of the circuit medical staff and those at the hospital, Perez sadly succumbed to his injuries on the morning of 11 June.”