After seven minutes Moussa raced clear of the floundering Adam El-Abd to burst into the penalty area and held off a challenge to bury a low drive past Simon Moore.
Coventry doubled their lead after 25 minutes when Nathan Delfouneso flicked on a Carl Baker corner and Andrew Webster reacted quickest to stab the ball home from six yards.
Substitute Wes Burns netted with a deflected header from an 82nd minute corner to give the hosts hope but it wasn't enough.
Groundstaff worked hard to ensure the game went ahead with heavy rain creating surface water and a gusty wind also making life difficult for the teams.
Sam Baldock hit the inside of a post for the Robins after 43 minutes after Coventry keeper Joe Murphy had misjudged a run out of his area and been rounded.
The hosts had second-half chances with the elements in their favour but Coventry worked hard to protect their lead against concerted late pressure.
In the night's other League One match, Darius Charles struck twice as bottom-club Stevenage claimed a hugely-important 3-1 victory over 10-man Gillingham to give their fight for survival a timely boost.
The Gills were forced to play a man light from the 21st minute after Elliott Hewitt's red card for deliberate handball and Boro took full advantage to move within two points of safety.
After a quiet start, the game exploded into life when Hewitt was sent off for handling Francois Zoko's shot on the line.
Zoko stepped up to casually roll in the resulting penalty but Boro should have lost their lead a couple of minutes later only for Cody McDonald to blaze over an open goal.
The hosts then went 2-0 up on the half-hour as Luke Freeman got away down the left and cut the ball back for Charles, whose effort was deflected in.
Gillingham thought they had a route back into the game when McDonald finished calmly only for Charles to grab his second three minutes later following a Freeman free-kick.