The 17-year-old impressed the Dutch side while on trial last year, but he could not sign a professional contract with Twente until he turns 18 next year.
In January Twente and Pirates reached an agreement to allow the youngster to play for Bucs in the second half of the season.
"I am sad but happy at the same time. Pirates is like home to me and I feel sad that I am leaving without having played for the senior team," Ntuli tells KickOff.com.
"I am happy though that I am going back to Holland because it’s every youngster's dream playing in Europe. They want me back to monitor my performance in their reserve team.
"They are waiting for me to turn 18 in February next year which means that I will qualify to sign a professional contract with the club,” he adds.