Dougherty tendered his resignation before the Local 98 Executive Board on Monday evening, the union said in a statement released Tuesday afternoon. "Johnny Doc," as he's known, led the union for nearly 30 years.
"The Executive Board reluctantly but unanimously accepted his resignation," the statement from union spokesman Frank Keel reads.
Local 98 Safety Director Mark Lynch was elected to serve as Interim Business Manager.
"I made this difficult but necessary decision to resign as Business Manager for the good of this union that has been my life's work and passion," Dougherty said in the statement. "I am leaving Local 98 in an incredibly strong position, financially and otherwise.
His resignation comes one day after he and City Councilman Bobby Henon were found guilty of conspiracy charges in a corruption trial.
Prosecutors said Dougherty kept Henon, a union electrician-turned-Philadelphia City Council member, on the payroll to help his union keep a tight grip on construction jobs.
In his first public appearance since the conviction of one of his most influential political supporters, Mayor Jim Kenney defended Dougherty.
"Never asked me to do anything wrong. I wouldn't have done it anyway, but always asked for his members and the organized labor," said Kenney. "I feel bad for them. I feel bad for their families."
Kenney, however, refused to comment whether he believed the court's decision that Dougherty bought Henon's influence to help the union out.
"I have my opinion, which I won't express," he said. My opinion is not important in this," Kenney added.
Kenney also did not say whether he believed Henon should resign. Under Pennsylvania law, Henon would not have to until sentencing.
While the majority of city council remained tight-lipped on the subject, one member did speak up.
"I think it would be best for him to resign at this point and focus on his appeal," said Councilwoman Maria Quinones-Sanchez.
Quinones-Sanchez said it's also her goal now to introduce legislation before the elected body to tackle the questions now raised about council members with secondary jobs outside office.
"I think it's not as simple as saying absolutely nothing but I think there are ways that we could require better disclosure," she said.
Along with Henon's $70,000 union job, he also roughly made $136,000 a year as a council member.
Their convictions follow a lengthy FBI investigation of activities within the chapter of the International Brotherhood of Electrical Workers that Dougherty led, but it will not mark the end of his legal woes.
Dougherty still faces at least one more federal trial based on charges in the sweeping 2019 indictment.
U.S. Attorney Jennifer Williams called the verdict "a strong message to the political power players of this city and any city that the citizens of Philadelphia will not tolerate public corruption as business as usual."
Jurors deliberated for several days last week before announcing a verdict Monday afternoon. The defendants' sentencing was scheduled for February.
The Associated Press contributed to this report.