His article in the Daily Record belittled the Scottish women's football team's 7-0 win Bosnia Herzegovina at Fir Park, which was shown on BBC Alba TV.
Cowan's column, which included a number of crude jokes, caused a storm of angry reaction on social media networks, and prompted the paper to add an editor's footnote to the online version, saying it should be "taken with a large pinch of salt".
However, BBC Scotland decided to ban him from Off the Ball today. Management are thought to have seen the column as unacceptable. It is not known yet if his absence is temporary or permanent.
Cowan, 44, was taken off air before the show went out at lunchtime, and was replaced at short notice by Annie McGuire, who has previously worked with Jim Traynor on his BBC Radio fans' call-in.
At the start of Off the Ball, co-host Stuart Cosgrove made no reference to the Daily Record column, but explained Cowan's absence by saying: "Alas, Tam's been delayed today…we're looking for him. He's out there somewhere."
Cowan's Record column began: "If I had my way, today's Premiership fixture between Motherwell and Ross County would have been cancelled. That's because Fir Park should have been torched on Thursday in order to cleanse the stadium after it played host to women's football. Why do they still persevere with this turgid spectacle? And why was it allowed anywhere near Motherwell's hallowed turf?"
He added: "Admittedly, I've not seen a lot of women's football…and I'm not having a pop at the people taking part. Just the other week, I bumped into a couple of women footballers (I've still got the bruises to prove it) and they were honestly two of the nicest blokes I've ever met…
"…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."
Among the critics on Twitter were Scottish Tory leader Ruth Davidson, who tweeted: "Fire up the Hillman Imp, Tam Cowan's going back to the 70s with his views on women's football."
SNP MSP Humza Yousaf added: "Invite Tam Cowan to come watch Glasgow Girls FC with me one day - he'll eat his words! Top quality football and great atmosphere too!"
Comedian Janey Godley said: "I like Tam Cowan but am disappointed he turned into a 70s misogynist ranter & tried to pass it off as 'comedy' Jim Davidson would be proud."
Leading novelist Ian Rankin added: "I wonder if anyone's told Tam Cowan that Charlotte Green read out the football results tonight (on Radio 5 Live - the first female to do so)."
After the backlash, the Record's online article was amended with the inclusion of an editor's note, which read: "Folks, we would like to point out Tam is a professional funnyman and what he has to say should be taken with a large pinch of salt. Also, his views are not necessarily those of the Daily Record as a whole."
The Record then tweeted: "Tam Cowan's piece today is HIS opinion. Read it and make up your own minds. Not publishing would be censorship."
Cowan is an ardent Motherwell fan and Daily Record columnist since 1998, producing a bi-weekly sports column and a weekly restaurant review.
He has presented Off The Ball for many years in tandem with his friend Cosgrove, who holds a senior position with Channel 4.
In February 2010, Cowan presented a six-part STV documentary series on literacy and numeracy difficulties among adults. In 2011, Cowan was also a co-presenter for STV's lifestyle magazine show The Hour, with Michelle McManus. The programme was axed four weeks after a move to a weekly prime time slot and a revamp led to low ratings.