Cowan was banned from presenting the show following the publication of a controversial column about women's football in the Daily Record last month.
The corporation has now said he will return to the airwaves on Saturday alongside Stuart Cosgrove.
A BBC Scotland spokesman said: "We've had several discussions with Tam following his newspaper column and he has made it clear to us that he made a serious error of judgement, for which he has apologised.
"He has also been reminded of his responsibilities as a broadcaster for BBC Scotland and, on that basis, he will be back co-presenting Off the Ball this weekend."
Cowan was accused of sexism and widely criticised after he referred to women's football as a "turgid spectacle" and described the players as "blokes" in his newspaper column.
In an article entitled: "A message from the dark Ages", he discussed the Scotland Women's international match with Bosnia, which attracted a crowd of less than 1000.
He wrote: "If women's football is so good, where the hell are all the supporters? Surely even the most fervent fans must agree it's time to chuck it?
"Face it, folks, nobody cares about women's football. There was barely a thousand inside the ground, shocking for an international in any sport, and I guess putting the girlies head-to-head with Emmerdale and Eastenders was a bit daft."
He also suggested Motherwell's Fir Park football stadium should be torched in order to "cleanse" it after it played host to the match.
He has since apologised for his comments and said he plans to make a donation to Scottish Women's Football.
In an apology in the Daily Record last month, he said: "The reaction to Saturday's piece on women's football has been quite incredible but I can assure you I meant it tongue-in-cheek.
"Hands up, it was a spectacular own goal and I want to apologise to anyone who was offended. Particularly Scottish women's football.
"In 15 years as a Daily Record columnist it has never been my objective to deliberately upset readers - that's a totally pointless exercise - and I've only tried to have a laugh, a joke and a carry-on.
"I've never expected anyone to take my column too seriously and I suppose my patter's a bit like a bride on her wedding day - something old, something new, something borrowed and, yes, something blue. More often than not, my sense of humour - just like my choice of music and my Nokia 3210 - is a wee bit old fashioned."
Followers of Cowan's radio show were split on whether he should have been allowed back on the air.
Freelance journalist Andy Davis tweeted: "Good to know that BBCScotland employees - like Tam Cowan - will receive only minor suspensions if they make very offensive sexist remarks."
Jonny McFarlane tweeted: "Tam Cowan is a lucky man to still be in a job.
"As a former disciplinary manager I think his article was clearly grounds for gross misconduct."