The Brazilian defender was involved in a sickening collision with Marlon Harewood and was taken to hospital for X-rays.
Thankfully, he was quickly given the all-clear and was able to return to Manchester with his team-mates following the dramatic 3-2 win.
Concern: Rafael was carried of on a stretcher after a clash with Marlon Harewood
However, as with all cases of concussion, United will ensure Rafael gets the correct break from physical contact and the 20-year-old will not travel to the south coast for this weekend's fourth-round tie.
Meanwhile, Javier Hernandez has admitted he should have had a hat-trick at Bloomfield Road.
The Mexican nabbed the equaliser 16 minutes from time, having failed to beat Richard Kingson with a similar opportunity not long after his introduction as a second-half substitute for Wayne Rooney.
Tough time: Rafael had only just returned from suspension, and had been caught out twice for Blackpool goals
It took his tally for the season to 10, but Hernandez might have also added to his side's lead during the 10 minutes of stoppage time.
'I could have had a hat-trick,' he said. 'But I always say the most important thing is that the team wins and we get the three points. It doesn't matter who scores. We just want the championship.'
Hernandez's exploits in his first season at Old Trafford have already earned him a place in the affections of United fans.
Yet even he is being put in the shade by Dimitar Berbatov, who added another two to his tally, taking him on to 20 for the campaign, which includes five in the last four days following the weekend hat-trick against Birmingham.
'Dimitar's form is unbelievable,' said Hernandez. 'He is a great player. He is improving every day on the training ground and also in the games. He is an excellent help for us.'
As a relative newcomer to the club, Hernandez is still learning about the comeback exploits for which United are so famous.
Yet he accepts the desire for victory within the camp runs as deep as their legendary self-belief.
'We didn't play so well in the first half but we know the quality of the team and we knew we could score three goals in the second half,' he said. 'We were always confident we could get back into the game.
King Dim: Berbatov came to United's rescue at Bloomfield Road
'Even if it had been 2-2 in the final minute we would have thought we could get a goal.'
United are now five points ahead of Arsenal and six in front of Manchester City, on whom they still have a game in hand.
They also remain unbeaten, a record they will not want to lose when they are next in Premier League action, against in-form Aston Villa next Tuesday.
'This win was very important,' said Hernandez. 'We knew with these three points we would be at the top with a bit of a difference between ourselves and the rest.'
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