The Liverpool manager took a gamble by substituting his star striker after 63 minutes with the scoreline locked at 1-1 against Fulham at Craven Cottage on Saturday, but his decision backfired when Fulham scored two more goals for a 3-1 victory.
Benitez said: "We needed to do something to protect the player. We were more or less in control of the game. If we had left him on the pitch maybe we would have lost the player for a month."
He added: "It was a difficult decision but we decided to start with him because he can do a proper warm-up. But we decided to take him out at 60 minutes. The last time he played 80 minutes it took him four days to be fit."
To make matters worse, they had Swiss defender Philipp Degen and captain Jamie Carragher sent off in what proved to be the worst possible preparation for their big European encounter.
It means the Spanish striker, who equalised Bobby Zamora's opening goal with a brilliant volley for his 10th league goal of the season, is touch and go to be fit for Wednesday's Group E match which could shape Liverpool's entire season.
Defeat could see them go out of the Champions League at the group stage and with Steven Gerrard doubtful with his groin injury and Glen Johnson suffering from a calf strain, the Liverpool injury list shows no sign of easing.