The Manchester United manager's praise came after Messi claimed the Ballon d'Or for the third consecutive year, beating team-mate Xavi and Real Madrid's Cristiano Ronaldo to the title.
Messi, man of the match in the Champions League final in 2011, also won the Spanish league, Spanish Supercopa, UEFA Super Cup and Club World Cup last year.
Ferguson, himself the recipient of the FIFA presidential award for services to football, said Messi could now be judged alongside the greats of world football through the ages, even though he is still only 24.
"Critics have always questioned whether players like Pele from the 50s could play today," said Ferguson.
"The answer to that is great players would play in any generation. Lionel Messi could play in the 1950s and the present day, as could Di Stefano, Pele, Maradona, Cruyff because they are all great players.
"Lionel Messi without question fits into that category."
Ferguson would know about Messi's abilities, having had his side outclassed by Messi in two separate Champions League Finals in three years.
Messi masterminded Barcelona's victory over Manchester United in 2009, setting up Samuel Eto'o for his side's first goal before scoring one more himself to seal the match 2-0.
The Argentinean then struck again two years later, scoring the second goal in Barcelona's 3-1 win at Wembley and winning the Man of the Match award.