The blustery conditions were far from conducive to football and it showed in a first half where neither side was able to string any moves of note together.
Caley Thistle did have the better of the chances with Dougie Imrie in particular twice going close in the opening 20 minutes, before Garry Wood's snapshot on the turn had to be palmed away to safety by Motherwell goalkeeper Graeme Smith.
It was Don Cowie who came the closest, however, with a free-kick from the angle that rebounded to safety via the crossbar on 31 minutes.
The visitors had rarely threatened, but two minutes later Stephen Hughes tried his luck from 25 yards only to see his effort skid a yard wide of Michael Fraser's post.
This brought about a period of pressure from Motherwell and Steven McGarry tested Fraser with a smart volley from just inside the box which the keeper touched around the post seven minutes from the interval.
After a largely non-eventful first half, the second burst to life with the opening goal only a minute after the restart.
Cowie's pass was not cleared by Keith Lasley, allowing Adam Rooney to poke the ball past Mark Reynolds and run on to fire low past Graeme Smith.
On the hour mark, Motherwell came close to equalising, but McGarry's shot was deflected inches wide by Ian Black.
At the other end, the visitors had Steven Hammell to thank for denying Grant Munro a clear shot on goal after the ball fell kindly to him inside the box.
That goal-saving tackle was to prove vital as the Steelmen drew level on 69 minutes, Chris Porter working a neat one-two with John Sutton before unleashing a low drive into the corner past Fraser.
This gave Motherwell the impetus to push on and seven minutes from time they took the lead with a wonderful 25-yard free-kick from Bob Malcolm that found the top corner of Fraser's goal.
It was a goal fit enough to win any game and so it proved to be the case as Motherwell held out for all three points.