The Cherry and Whites announced in November that Fearns, 28, would move to Kingsholm on a three-year deal after the conclusion of the 2016-17 season.
But Lyon offered him "significantly increased personal terms".
Gloucester CEO Steven Vaughan said the club had initially sought legal advice but have now received compensation.
Vaughan said: "Naturally the club took the best legal advice on the situation, but as soon as it became apparent the player wanted to remain in France, efforts immediately turned to getting the best possible deal for the club to allow us to move on in a stronger position.
"I am very happy at the outcome and we have agreed significant compensation that will all be used on strengthening the playing group further."
Englishman Fearns joined Lyon in 2015 and was named player of the season as he helped them win promotion to France's top flight in his first season, while he made 22 appearances this term.
Gloucester have confirmed back-row forward Carl Fearns will remain with Lyon, despite signing a deal to move to the Premiership side this summer.