Maria Alejandra Vicuna announced her resignation Tuesday on Twitter, saying the South American country did not deserve the "instability" caused by the crisis.
In Ecuador, the vice-president can only be sacked through an impeachment process in the national assembly, which last week called on her to resign.
Vicuna has been in the post for just over a year. She replaced Moreno's running mate, Jorge Glas, convicted and jailed over his involvement in the massive Odebrecht bribes scandal.
The allegations against Vicuna come from a former aide, Angel Sagbay, who said last week that while working as Vicuna's advisor in 2012 and 2013 he regularly banked deposits -- totalling around $20,000 -- in Vicuna's account that he claims were kickbacks.
Prosecutors are investigating the corruption allegations and Vicuna said she was confident she will be cleared by the courts.
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