Shoya Nakajima's opener for Japan was cancelled out by Angel Mena during the first half of the Group C clash in Belo Horizonte.
Ecuador and Japan looked for a winner but ended up playing out a draw that suited neither team as they bid to reach the quarter-finals.
A victory would have seen either advance as one of the best third-placed teams, however they are instead both going home.
Both teams made a relatively scrappy start, trying their luck from distance in the opening stages.
But Japan took the lead in the 15th minute through Nakajima's fine strike.
Ecuador goalkeeper Alexander Dominguez swept a ball in behind straight to Nakajima, whose 25-yard effort went in via the underside of the crossbar with the keeper stranded.
Enner Valencia should have brought Ecuador level eight minutes later, but his shot from close range was tame and well saved by a scrambling Eiji Kawashima after a poor turnover by Japan.
However, Ecuador equalised 10 minutes before half-time thanks to Mena.
Robert Arboleda had a volley well saved by Kawashima, but Mena was on hand to tap away the rebound and make it 1-1.
Ecuador made the better start to the second half, but Japan almost restored their lead, Naomichi Ueda heading a set-piece straight at Dominguez in the 66th minute.
Pedro Pablo Velasco fired wide for Ecuador midway through the second half and both teams pushed in the closing stages, but struggled to create clear-cut opportunities, Daizen Maeda squandering a one-on-one chance for Japan in the 90th minute.
What does it mean? Paraguay in luck
Ecuador and Japan needed a win to progress as one of the best third-placed teams. Instead, they drew, allowing Paraguay to advance to an unlikely quarter-final against Brazil.
Ecuador's struggles continue
They came into the tournament on a four-match winless run and that continued for Ecuador at the Copa America. Ecuador have won only two of their 19 Copa America games since 2004.
Japan fall short despite good signs
Having taken a relatively young squad to the tournament, Japan were solid without managing the one win they needed. The 4-0 loss to Chile was harsh on them, while they improved in draws with Uruguay and Ecuador.
Japan look ahead to the EAFF Football Championship in December, while Ecuador have plenty of reflecting to do after a poor campaign.