Di Stefano, 88, had been under supervision at Madrid's Gregorio Maranon Hospital after suffering a heart attack on Saturday but the two-time Ballon d'Or winner died two days later.
Tributes have been flowing in for the Argentine-born forward, who scored 308 goals in 396 appearances for Real and won 16 trophies with the Madrid outfit, and Ferguson is the latest football identity to have paid their respects.
"The great question which always comes up is 'who are the greatest players?'" Ferguson told Sky Sports News.
"There is a phalanx of great ones – [Johan] Cruyff, [Diego] Maradona, Pele, [Ferenc] Puskas and Di Stefano. Di Stefano was one of the greatest in my mind.
"He had fantastic balance and poise – if you look at one of the goals he scored against Eintracht Frankfurt it was completely what we were talking about – the balance he had. Unbelievable, he was."
Di Stefano - winner of five consecutive European cups with Real between 1956 and 1960 - went on to coach the iconic club in two separate spells.
In his first stint, Di Stefano came up against Ferguson's Aberdeen in the 1983 European Cup Winners' Cup final, which was won by the Scottish club 2-1 after extra time in Sweden - a meeting the former United boss remembers clearly.
"It was an honour to come up against Di Stefano," he said. "What I did, out of respect for him, was I bought a bottle of Scottish Malt whisky and gave it to him the night before the match when the two teams had an opportunity to train on the pitch at the venue for the final.
"We were second, they were first. When he came off, they were coming down the tunnel and I said 'Mr Di Stefano, I'd like to give you this gift.' He was taken aback, he was really taken aback.
Ferguson added: "He said, 'Aberdeen are a team that money can't buy. They have a soul, and a family spirit'. Those words – you couldn't say any more, in terms of praise for a football team. It was very generous of him.
"He was always the focus of Real Madrid wherever they went. He had a fantastic life and I'm proud to have been associated with him in a small way."