Lopes was injured as he dived at the feet of Barcelona's Philippe Coutinho in the 22nd minute of the round of 16, second leg UEFA Champions League match in midweek.
Although he initially looked as if he was going off, Lopes remained on the pitch for another 11 minutes before being substituted.
In a statement to Reuters, FIFPro claimed the incident 'again highlights failures in the current concussion protocol in professional football'. They added that these failures 'risk seriously damaging the health of players'.
UEFA and Lyon did not immediately reply to requests for comment.
FIFPro called for an independent doctor at matches to help decide whether a player with suspected concussion should continue, rather than leaving the decision with team doctors as happens at present.
They added that a temporary substitute should be allowed on the field to allow medical staff time to review whether a player has concussion.
"We are concerned that while such procedures are successfully employed in multiple sports they have not been adopted by professional football," the statement read.
In their protocol for dealing with suspected concussion, UEFA say that the referee should stop the game for up to three minutes 'to allow the injured player to be assessed by the team doctor'.
"A player will only be allowed to continue playing on specific confirmation by the team doctor to the referee of the player's fitness to carry on," they said.
FIFPro's own guidelines warn of the dangers of continuing to play while concussed.
"A second concussion can lead to a dangerous swelling of the brain if a player has not fully recovered from the first concussion," they say.
FIFPro guidelines also say that concussion can occur without a direct hit on the head, as happened in the case of Lopes who crashed to the ground in the collision with Coutinho and hit his shoulder hard on the pitch.
