The city maintains the charge became irrelevant as more officers complied, but it comes a month after a judge humiliated Mayor Lori Lightfoot by delaying her December 31 deadline.
In October, Chicago had sued the Fraternal Order of Police Lodge 7, accusing President John Catanzara of supporting an "illegal strike" by encouraging officers to disregard the order.
After withdrawing the claim, Lightfoot promised Wednesday that if union leaders resumed talks of an "illegal work stoppage" over the mandate, the city would return to court.
Chicago's mandate for police brought attention to the cop shortage when the city is dealing with increasing violent crime.
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So far this year, the city has seen 739 murders, a three percent increase from last year's already raised figure and a 60 percent jump from 2019. Shootings are up nine percent and 66 percent from 2020 and 2019 each.
Lightfoot's questionable reputation with cops was aggravated by the murder of Officer Ella French, with many turning their backs on the mayor when she visited French's injured partner in the hospital.
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Having already defunded the police department, Lightfoot has now supported pushing more money into it amid worsening corruption in her city.
The city insisted that those who didn't comply with the vaccine mandate would eventually be placed on "no-pay status."
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In public statements and on social media, Catanzaro prompted police to violate the order, telling them, "do not fall for it, hold the line." The union also sued.
Lightfoot said the order passed to protect officers and the public, and the Democrat Mayor blamed the cop union for "insurrection" for defying her orders.
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More than 460 law enforcement officers have died of COVID-19, including four in Chicago, according to the Officer Down Memorial Page.
"From day one when this requirement was announced in August, this entire process has been and will continue to be about protecting the lives and safety of all Chicagoans," Lightfoot said in a statement.
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"The data shows that we are succeeding in that mission, and that police officers recognize that protecting and serving in the times of global pandemic means ensuring that they are vaccinated against COVID-19."
Police have lingered behind other city departments in complying with steps in the city's vaccine requirements.
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Employees must first state their vaccine status and then get vaccinated by year's end.
Still, the percentage of the police department employees reporting their status increased from about 65 percent in October to about 87 percent this week. Most other city departments are near or at 100 percent compliance.
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