Steve Carter said he become physically sick last month after reading allegations in The New York Times (NYT) that Mr Hybels had engaged in sexual impropriety with a former assistant, Pat Baranowski.
Mr Carter, 38, told the Religion News Service (RNS): "I felt like my body was shutting down."
The NYT article, which Mr Carter described as "a breaking point", was published five months after the Chicago Tribune revealed claims of misconduct against Mr Hybels involving a number of women.
The 66-year-old denied any wrongdoing but apologised for being "unwise" and potentially misleading people.
In one case, a woman suggested Hybels summoned her to his hotel room and kissed her while on a trip to Sweden in 1998.
Another accused him of "a lingering hug" which made her feel uncomfortable while another claim suggested he'd invited a woman to his house, but only while his wife was away.
Mr Hybels, who had previously announced his intention to retire in autumn 2018, stepped down early following accusations published in the Tribune.
Willow Creek has faced criticism over its handling of the claims made against Mr Hybels.
In a statement released three days after the NYT article, the board of elders admitted an investigation in Mr Hybels was "flawed" and they apologised for their response to the accusations.
Mr Carter, who had been due to succeed him as lead teaching pastor, announced he would resign. The board of elders and fellow pastor Heather Larson also tendered their resignations.
Speaking with the RNS, Mr Carter said he believed Willow Creek could be saved but the church must acknowledge its failings and confess its sin.
He added: "I think the people of Willow are really strong. They love the church."
Reflecting on his longstanding relationship with Mr Hybels, Mr Carter added: "I have 1,000 good stories with Bill. And I have ten wounds from him."
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