British Lion Tom Shanklin replaces Henson in the starting line-up at outside centre with Cardiff Blues team-mate Jamie Roberts switching to inside centre with Andrew Bishop coming onto the bench.
This is the latest set-back for the Wales and Ospreys star who has been dogged by problems both on and off the pitch.
Henson has made just nine starts in three years for Wales since damaging his shoulder playing for the British Lions in 2005.
Groin surgery and suspension hampered 2006 while a year later, the 26-year-old tore cruciate knee ligaments before missing out on the World Cup that year with an Achilles problem.
Henson returned from a broken hand to spearhead last year's Slam success only to sit out the next six months following ankle surgery.
He then withdrew on the eve of the 2008 autumn series after the Achilles problem reared up once again before this latest set-back.
Wales coach Warren Gatland kept his faith in Henson who has been a lucky charm in the Six Nations having never lost in ten championship games when he has started.
Gatland said: "Gavin just felt his calf tightening in training. There is no point making it a major problem that would keep him out for six or eight weeks."
Wales (v Scotland): Lee Byrne; Leigh Halfpenny, Tom Shanklin, Jamie Roberts, Shane Williams; Stephen Jones, Mike Phillips; Gethin Jenkins, Matthew Rees, Adam Jones, Ian Gough, Alun Wyn Jones, Ryan Jones (capt), Andy Powell, Martyn Williams. Replacements: John Yapp, Huw Bennett, Luke Charteris, Dafydd Jones, Dwayne Peel, James Hook, Andrew Bishop.