Nsiala has made 13 appearances since joining the Reds in January.
"We're delighted to be keeping Toto," said boss Paul Cook in a club statement. "He's improving all the time and has come on hugely from when I first came into the club.
"He's a really commanding centre-half and we're really pleased with how he's shaping up. Long may it continue.
"Everton have been good enough to let him come here to learn as a young player and we're thankful they've allowed him to stay for longer."