Last Saturday, Cameron Bancroft was videoed tampering with the ball during the third Test with South Africa, and it has now been revealed that vice-captain David Warner came up with the idea, which was then given the green light by skipper Steve Smith.
The trio have since been given sanctions by Cricket Australia, but the governing body said that Lehmann was not aware of any plan to change the condition of the ball until the players were on the pitch.
However, the 48-year-old has opted to resign from his position after the fourth and final Test with the Proteas, ending a near five-year spell with the Baggy Greens.
Lehmann is quoted by Cricinfo as saying: "Life on the road means a lot of time away from loved ones and after speaking to my family, it is the right time to step away.
"Speaking to the players and saying goodbye is the toughest thing I have had to do. It's been happening for a few days and you think you can keep going but the amount of abuse just takes it toll. They made a mistake."
Earlier on Thursday, Smith and Bancroft held press conferences to apologise for their roles in the incident, while Warner released a statement on social media.