The 18-year-old, surprisingly picked ahead of Wes Brown in the starting line-up, glittered in United's Champions League stroll over Aalborg before having to leave the field in the second half with a knock.
"We have great hopes for the lad," said Ferguson. "He has impressed us a lot.
"Some people might have been a bit surprised I picked him over Wes Brown but I feel the boy has something special."
Rafael, his twin brother Fabio and midfielder Rodrigo Possebon all came to United's attention during a youth tournament in Hong Kong three years ago.
A member of the Brazil Under-17 side at last year's FIFA World Cup, Rafael signed for the Old Trafford outfit in January this year but due to work permit regulations was not able to play a competitive game until this summer.
"Rafael has no fear of playing and has great belief in himself," said Ferguson.
"He is only 18 but he has started very well. He did well against Middlesbrough last week and he has progressed again.
"He is really positive and has a great chance in the future."
Meanwhile, Fabio Capello will be a more than interested observer of Wayne Rooney's ankle injury, which may be a cause for concern for England.
Rafael Da Silva's first Champions League start also ended with him limping off the field while goalscorer Rooney left proceedings feeling pain in his ankle.
Sir Alex Ferguson has already virtually written him out of United's league encounter with Blackburn at Ewood Park on Saturday.
"Wayne felt his ankle," confirmed Ferguson.
"We hope it is not ligament trouble - but he is doubtful for Saturday, I would imagine."
Capello is due to name his England squad for the World Cup qualifiers with Kazakhstan and Belarus on Sunday and ligament damage would surely rule Rooney out of both.
Scholes is unlikely to be available again until the visit to Tottenham on December 13, which comes immediately before United head to Japan for the World Club Championship.
It means Scholes will miss the rest of his side's Champions League group campaign, plus key Premier League away games at Everton, Arsenal and Manchester City.
In total the 33-year-old could miss 16 matches from United's season and Michael Carrick and Owen Hargreaves are currently on the sidelines too.