However, he admits those clay court losses did get to him.
"The way he played or plays against me has always been extremely difficult for me," Federer said at an event in Perth, ahead of his appearance at the Hopman Cup.
"Plus, I played way too many clay court matches against him. That kind of scarred me.
"He beat me a lot of times in those finals time and time again. He showed me what he can do and that's why I hope he can come back [from injury] extremely strong again, because I think the world of Rafa and his game.
"It's quite extraordinary actually and his fighting spirit and his professionalism that he brings to the game.
"I've really enjoyed watching him and it's been tough against him, so every match I've won against him I almost count it double for me."
Federer, who has not played since re-injuring his surgically repaired left knee at Wimbledon in July, will make his tournament return for representing Switzerland at the Hopman Cup alongside Belinda Bencic.
The 17-time Grand Slam champion has never spent so long away from the sport since turning professional and isn't used to dealing with serious injury.
On the other hand, Nadal is much more accustomed to his body breaking down. A wrist injury ended his 2016 French Open campaign and it played up again in October, curtailing his season altogether.
Federer's time on the side-lines has only added to the respect he has for his long-time foe.
"Now I understand a little bit, when guys are injured, how hard it is to come back and how much patience you have to bring to the table," said Federer. "It's not easy and I admire the guys who have done it before me, like Rafa for instance.
"He's always come back and it seemed like nothing. Every time he came back, he had success, so I hope it's going to be the same for me."
Federer admitted he was both relieved and sad, after making a hot return from injury at the Hopman Cup on Monday night.
He entered the mixed-teams tournament, thinking he might be a tad rusty after spending the previous six months sidelined with a knee injury. But the veteran cracked a series of stunning winners to secure a 6-3 6-4 win in just 61 minutes over Great Britain's Dan Evans.
Federer was overcome with emotion, when he received a standing ovation from the Perth Arena crowd as he made his way to the court.
He was pleasantly surprised by how well he played, but now that he's got the taste of competitive tennis again, he wants a lot more.
"I'd like to live it again," said Federer. "I'm a little bit sad it's over, because it was so nice out there.
"I was actually quite emotional. When I walked down, I was like, 'Oh my god, this is better than I thought it would be'.
"It felt good, putting the match shirt back on and serving first, and then trying to serve it out at the end.
"They're the moments I miss the most, even though those are the ones that make you nervous.
"That's why you play tennis for. I thought, for a first match, it was great, because my expectations were obviously quite low."
The triumph gave Switzerland a 1-0 lead in the tie, ahead of Belinda Bencic's clash with Great Britain's Heather Watson.
The Swiss didn't look hindered one bit in his opening tie, even leaping high into the air to smash a winner in the second set. The 35-year-old wants to keep playing for another two or three years, and said he wasn't troubled by his knee in his return.
"For three or four weeks now, I've stopped thinking of it, because I don't have any reactions anymore," Federer said. "I don't have any pain.
"It's been nice that I was able to get rid of that early."
Although Federer unleashed the occasional shank against Evans, he also produced a series of stunning winners.
He also showcased his trademark class, offering some kind words to a lineswoman, after she got struck in the head by an Evans ace.
