The 82-year-old Miyazaki, co-founder of the celebrated anime house Ghibli, came out of retirement to make "How Do You Live?".
It was years in production, with the studio taking the unusual step of keeping details about the plot tightly under wraps and offering minimal publicity.
The only clue about the storyline was a poster featuring a hand-sketched, bird-like creature with an eye nestled below its beak.
"It was a very Ghibli-esque movie," university student Eisaku Kimura, 21, told AFP after watching a morning screening of the film in the trendy Shibuya district.
"It's not like I felt anything special about it just because it was his last work, but I saw a lot of (Miyazaki) in the movie for sure, and it was exciting."
"How Do You Live?" was inspired by a 1937 book of the same title, but the studio said previously the movie would be entirely different.
The film is about a boy who moves to the countryside with his father following the death of his mother.
There, he meets a heron, who transports him to an alternate universe where the mystery of his mother's death slowly unravels.
"It's such a crazy mixture of all the Ghibli movies I've seen before," Valeriia Matveeva, an English teacher from Russia, 30, told AFP.
"I think it takes the best of it, and I think it's kind of scary at times but it's also magical. Because there was no promotion, I had no idea what to think about it, but it was good."
Miyazaki has built a cult following with his fantastical depictions of nature and machinery, and beloved characters like the cuddly forest spirit creature Totoro.
His film "Spirited Away," about a girl who gets lost in a mysterious world and tries to save her parents, who are turned into pigs, won an Oscar for best animated feature in 2003.
In 2013, Miyazaki said he would no longer make feature-length films, as he could not maintain the hectic intensity of his perfectionist approach to work.
However, in an about-turn four years later, his production company said he was coming out of retirement to make what would be "his final film, considering his age."