Cowan was dropped from Saturday's Off The Ball show on Radio Scotland, which he co-presents with Stuart Cosgrove, and is now due to meet with BBC Scotland's Commissioning Editor Ewan Angus to discuss his future after the comments in his Daily Record column were criticised.
He has now apologised, saying 'this has not been my finest hour and a half'. He also plans to make a donation to Scottish Women's Football.
He wrote in today's Daily Record: "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 OG 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."
He added: "As a married man with a lovely wee daughter, I was hurt by the 'misogynist' nonsense.
"I've often said I wouldn't open the curtains if a women's football match was being played in my back garden.
"From now on, the curtains will probably still remain shut. But so, I promise, will my mouth."
The Record took a circumspect view on Cowan's writing, suggesting his views "should be taken with a pinch of salt". However, his suspension suggests the BBC is taking a more serious view.
After describing some women footballers as "blokes", Cowan wrote of the recent women's international at Motherwell's Fir Park ground: "Face it, folks, nobody cares about women's football.
"There was barely a thousand there ... and I guess putting the girlies head-to-head with Emmerdale and EastEnders was a bit daft."
Maureen McGonigle, executive administrator for Scottish Women's Football, said the comments were "very narrow-minded".
A spokesman for BBC Scotland said: "Ewan Angus will speak to Tam during the week. Until then, the position remains the same."