The Belgium international, who joined Liverpool last month only to be handed back to Lille on a temporary basis, was on target in the 69th minute after the visitors had been awarded a controversial penalty following a challenge on Origi that resulted in the dismissal of Dennis Appiah.
Having sent Remy Vercoutre the wrong way to convert from 12 yards, the striker's night ended in concern as he limped off with an apparent muscle injury.
Caen, playing in Le Mans while their stadium is used for the World Equestrian games, carried more of an attacking threat in the opening half and would have been ahead had their finishing matched their build-up play.
The visitors became more of a force as the match wore on, but it appeared a generous decision from referee Sebastien Desiage that provided Lille with the opportunity to register the game's only goal.
With Origi bearing down on goal, full-back Appiah challenged the Lille striker on the edge of the penalty area, a tackle that was punished by the official with a straight red card but was later shown to be a clean one on television replays.
Origi's penalty conversion opened Lille's account for the season after they were held to a 0-0 draw by Metz on the opening weekend.
Caen came close to snatching what would have been a deserved point in the closing seconds as Bengali-Fode Koita rose above his marker, but the attacker's header was cleared off the line.
The only sour point of the night for Lille was the late injury for their match-winner, casting doubt over his participation in the first leg of the UEFA Champions League play-off with Porto on Wednesday.
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