President Lenin Moreno announced Zevallos's resignation on Twitter, after the move prompted a major backlash. He posted the minister's resignation letter, which explained that his decision to step down was due to "the current political climate." Zevallos added that he was also stepping down to "allow the National Vaccination Campaign to continue."
Zevallos, who oversaw Ecuador's approach to the pandemic, came under fire after it was revealed the Health Ministry had invited a university rector to receive a vaccine before health workers and the elderly.
Zevallos is the third South American health minister to resign after similar vaccine access scandals.
Peru's Pilar Mazzetti resigned on February 13 after it was revealed a group of politicians, including former president Martin Vizcarra, had been given access to the vaccine ahead of other groups.
On February 20, Argentina's health minister, Gines Gonzalez Garcia, also stepped down after a journalist revealed he was part of a "VIP group" that was vaccinated by the health ministry outside the regular vaccination campaign.
Latin American countries were left scrambling for vaccines earlier this year. Ecuador began its inoculation campaign in January using the Pfizer/BioNTech vaccine.
The country has reported 281,169 total Covid-19 cases and 15,669 deaths, according to Johns Hopkins University.