A win for either team would have guaranteed them a place in the last eight and Japan had the better of the early stages and took the lead in 15 minutes when Shoya Nakajima scored from 25 meters out.
Ecuador equalised 20 minutes later when Angel Mena pounced on a parried shot to touch home from close range and the South Americans grew into the game, especially in the second half, when their long ball game troubled the young Japanese side.
With both sides needing to win, the game was open and lively, even though it was played in front of the lowest crowd of the tournament so far, only 9,729 people present at the Mineirao stadium in Belo Horizonte.
Both sides had chances to get the goal that would take them through, with substitute Ayrton Preciado slipping a great chance just outside the post for Ecuador in stoppage time, just moments after Japan watched the referee chalk off a goal for offside.
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Group C winners Uruguay, who beat reigning Copa America champions Chile 1-0, will face Peru on Saturday, while Chile will take on Group B winners Colombia, the only team to win all three of their first-round games, the day before.
Hosts Brazil play Paraguay in Porto Alegre in the first quarter-final on Thursday, and Venezuela face Argentina at the Maracana stadium in Rio on Friday.
(Reporting by Andrew Downie; Editing by Peter Rutherford)
