The Brazilian forward was taken away on a stretcher after just 25 minutes after twisting his ankle badly as he strained to make a cross at the byline, with a club statement revealing he has a tear to a "tendon of his right ankle.
Further tests will be conducted on Friday but after the match Barca coach Gerardo Martino played the blow.
"The situation didn't look good when you saw it happen and you thought he might be out for a while but thank God it is not as serious as it appeared and he'll be back playing soon," he said.
"The doctors after the game have said it is not so bad and so if tests confirm it then it is not something serious."
Despite the injury Barca eased into the last eight thanks to a double from Lionel Messi, with his second goal, a magnificent solo effort, providing the highlight of the contest.
However, the little Argentinian should have found the net after just five minutes, flashing a side-footed shot just past the near post after a good lay off by Cristian Tello.
Minutes later the roles were reversed, with Messi setting up his team-mate with a wonderful floated free-kick to the back post, but an unmarked Tello snatched at the shot and sliced horribly wide.
Getafe started the game slowly but began to look more dangerous on the counter attack and came close to breaking the deadlock when Pinto pulled off a great save to deny Juan Rodriguez on the volley.
Alexis Sanchez, who came on to replace the injured Neymar, was presented with a good chance at the back post but just like Tello he failed to make a good connection with the ball.
But Barcelona finally took the lead just before the break when Messi turned home Tello’s low, driven cross into the six-yard box to put the contest well and truly out of sight for Getafe.
Tello was afforded another good opportunity to add his name to the scoresheet but once again he lacked composure on the ball and sliced his effort by the near post.
Messi doubled his tally in the second half with a magnificent solo effort, jinking through the tackles of several Getafe players to round the keeper and finish into the empty net.
The Barcelona number 10 was denied his hat trick just seconds later, with Codina this time getting the better of Messi, blocking the shot from close range with his legs.
And Codina pulled off an even better stop with just minutes remaining, spreading his legs to stop Messi from finally scoring his and Barcelona’s third of the game, although the gloss had already been applied to the aggregate score.