The breathtaking win for Japan meant they topped Group E, followed by Spain in second who finished ahead of third-placed Germany only on goal difference.
Japan fans were in tears at the end of the match which gives them a chance to go further than they ever have before at a World Cup.
"There were many fans who came all the way from Japan, as well as those that stayed behind in Japan," coach Moriyasu said.
"We didn't have any danger in the first half, then in the second half, I told them during halftime to be cautious, because they would attack in the second half, they don't have anything to lose," he said.
Japan defender Kou Itakura was shown his second yellow card of the tournament and will be suspended for the Croatia match.