The 25-year-old fired home in the 43rd minute to break the deadlock and put his nation on course for a possible first ever appearance in the quarter-finals.
Maeda was quickest to react when the ball dropped inside the six yard box from a corner kick as Japan took a one-goal lead into the interval.
Celtic team-mate Josip Juranovic and Rangers rival Borna Barisic both started for Croatia but Japan were well worth their lead, with Maeda's performance in attack earning rave reviews from BBC pundits.
Former England defender Rio Ferdinand said: "He's been an absolute livewire. I think it's only his second international goal.
He's looked like a man possessed up there.
"You wouldn't want to play against that, H'es running around, making it difficult for you.
"With and without the ball he's an absolute nuisance.
"In the first minute of the game he's closed the keeper down. You know you're in for it now.
"That's the catalyst for the others to come from behind."
Maeda also went close to scoring earlier in the half but he just failed to connect with a low ball across the near post.
"His movement to get across the front of [Dejan] Lovren was fantastic there," Ferdinand added.
"Top drawer movement, [he] just didn't have the final piece of the jigsaw there.
"What I like about him, he's always on the move."
Former England striker Alan Shearer was also impressed with Maeda's contribution, adding: "He's been a nightmare for them at the back, hasn't he? He's got too much energy for them."