Mr Thomson has strenuously denied allegations that he groped Labour MP Paul Sweeney in a House of Commons bar last October, but confirmed yesterday that he would not seek re-election on December 12.
The 32-year-old, who led Boris Johnson's leadership campaign in Scotland, is still under investigation by Commons authorities over the alleged incident after it was first raised in 2018.
Mr Sweeney initially remained anonymous after first making his complaint but decided to go public with his allegations last weekend.
Scots Tory leader Jackson Carlaw said today he was "obviously disappointed" that Mr Thomson had chosen to stand down but claimed it would not harm his party's chances of retaining Aberdeen South.
Douglas Lumsden, the co-leader of Aberdeen City Council, will now contest the seat for the Tories, who have a majority of 4,752 over the SNP.
Speaking at a campaign event in Hamilton town centre today, Mr Carlaw said: "I am obviously disappointed that Ross has withdrawn from the contest, but it was entirely his own decision.
"These were allegations that were made some time ago that the House of Commons has been investigating. They have been considering all the evidence - I haven't see it.
"They have not as yet come to a conclusion, but Ross decided the appropriate thing to do was to withdraw from the contest, and we have accepted that.
"We have now selected a new candidate, Doug Lumsden, who I believe will fight and retain the seat.
"Ross did not want this to become a huge distraction. I support the decision he has arrived at.
He added: "The disciplinary process for all members of parliament is one run from Westminster, not from in Scotland. That process is on-going. The key allegation made by the Labour MP was one made to House of Commons authorities.
"In the exchange of texts I've had with Ross, I understand it was entirely his own decision. I think he found the burden on him to be quite intolerable. He has been contesting these allegations all the way through. He denies them. I did not speak to anyone in the local association on the issue."
In a statement published yesterday, Mr Thomson said:
"Anonymous and malicious allegations this year have made my life a living hell. It has been nothing short of traumatic. I have suffered a level of personal abuse that has affected my health, my mental well-being and my staff. It has been a level of abuse that I never imagined possible.
"I always believed that politics was about noble pursuits and doing what you believed to be best for your country. My experience is that our politics is now so poisonous that we will never attract good, honest and decent people in the first place.
"I have there fore made the most difficult decision that I could ever make. I have decided that I will stand down as the Scottish Conservative and Unionist candidate for Aberdeen South."