The 29-year-old suffered the injury during the first half of the Cherry and Whites' 22-16 Guinness Premiership victory over Saracens on Saturday.
Vainikolo has made 17 appearances in all competitions this season and has scored eight tries. He won the first of his five England caps against Wales in the RBS 6 Nations last year.
Gloucester head coach Dean Ryan said: "Les is a massive part of our squad, not just for his on-field contributions but because his personality is such an integral and vital part of the group.
"It will naturally leave a very significant gap - and with the current injuries we have in the squad, at the moment this could not have come at a worse time.
"Les has undergone surgery and when it is appropriate he will begin his rehabilitation process.
"But we appreciate it will be a long road - and he will have all the support he needs from everyone associated with the club."