Kirk Ramsay resigned as chairman of Stow College in Glasgow, just days after the SNP minister demanded he quit over the affair.
He announced his decision at a board meeting last night after earlier apologising for his actions and insisting he had done nothing wrong.
Mr Ramsay now plans to clear his name and wants the Scottish Parliament's Education Committee to launch a formal inquiry.
In a statement, Mr Ramsay said: "My resignation follows an unwarranted personal attack on me by Michael Russell MSP.
"My passion and commitment for Stow College, and the college education sector as a whole, is too great for me to allow any perceived error on my part to be allowed to inflict damage on the college, its students or staff, executives and board.
"I remain firm in my belief that I have done nothing wrong and intend to clear my name. I especially look forward to meeting with the Parliament's Education Committee should it decide to launch a formal inquiry, which I sincerely hope they do.
"I look forward to returning to make useful contributions to college education in due course."
Mr Ramsay said his contribution to the development of Stow College was both major and undisputed and had brought real benefits.
The board accepted his decision with "great sadness", adding: "We accept that, in the circumstances, it is the honourable thing to do. It is typical of Kirk to put the college, its students and staff first and, by resigning at this time, he has once again shown his commitment to Stow College."
Mr Russell last week took the unprecedented step of writing to every college principal and chairman in Scotland to highlight the recording.
In heated exchanges yesterday with opposition politicians at Holyrood, who accused him of trying to bully Mr Ramsay out of office, Mr Russell refused to apologise.
Insisting the secretly taped meeting with senior figures in further education had been positive, Mr Russell added: "Anything that diminishes those debates, such as secret recording, is to be regretted.
"I'm confident the collaborative efforts we are making to change the college sector for the good not of individuals in the sector but for young people is on course. The Scottish Government believes the college sector, like any other, needs to be led and governed by people of the highest quality and standards.
"Chief among their attributes must always be mutual trust and respect."
In his previous letter, Mr Russell questioned Mr Ramsay's suitability for a post on the board of Stow.
It states: "It appears that an unauthorised audio recording was made of the event, without my knowledge or the courtesy of notifying those in attendance. I'm informed that this recording has now been distributed by Mr Ramsay.
"I am afraid I do not regard Mr Ramsay's actions as consistent in any way with the protocol expected at such an event or of the standards I expect [of the chairman of a board of management of] any college."
On Friday, Mr Russell said Mr Ramsay's conduct had caused him to question his confidence in the Stow College chairman. Mr Ramsay hit back with his own letter to college leaders expressing his "disappointment" at the actions. He said: "Rather than take detailed notes of Mr Russell's speech, I recorded his comments. This recording was solely for my own use and for others who could not attend.
"I am extremely disappointed that Mr Russell has used his position to seek to exert such control, influence and power both privately, but also so publicly."
The meeting was seen as an opportunity for college leaders to speak to Mr Russell about restructuring, which has led to a wave of mergers.
Some do not agree with the reforms amid savage cuts to teaching budgets of £73 million, a reduction in student numbers and more than 1000 job losses.
There have also been reports of thousands of names on college waiting lists.
The meeting last month was said by those present to have been largely constructive.
Stow previously courted controversy by pulling out of a merger that resulted in a number of Glasgow colleges join forces to become the City of Glasgow College.
Stow decided to stay as a single institution, although it is now considering merging with other colleges in the city.
A Scottish Government spokesman said: "Mr Russell's position has been clear throughout. This has always been a matter for Mr Ramsay and the board of Stow College."