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Goalkeeper Emi Martinez made two saves for the reigning champions in the shootout following a 1-1 draw in regulation time.
Group winners Venezuela, who beat Jamaica 3-0, take on Canada in the last eight.
Victory gave Ecuador, who were beaten by Venezuela in their Group B opener, their first points of the tournament.
In other qualifiers, Paraguay drew 0-0 with Peru while Colombia claimed a 1-0 home win over Venezuela.
The quake struck at a depth of 66.4 km (41.3 miles) about 10 km (6.2 miles) from the city of Balao in the province of Guayas.
A draw would have done against Senegal, but Ecuador paid for two lapses in concentration.
Ecuador need to win or draw to progress but will remain in contention if they lose and Qatar upset the Dutch, who were leading 1-0 at halftime.
The result means hosts Qatar have been knocked out from the tournament.
One of the pandas sniffed at the two flags and then placed its paw on the Ecuador flag, thus predicting that the winner could be Ecuador.
The striker nicknamed 'Superman' scored a brace to help his side to 2-0 win over Qatar.