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Alcaraz breezed past Alexander Zverev in just 62 minutes in the Madrid final as he became the second-youngest player to win two ATP Masters 1000 titles, after also triumphing in Miami in March.
The 19 year-old is also the youngest five-time ATP Tour winner since Nadal won seven titles by the same age in 2004-2005.
Alcaraz had already made more history en route to the final in the Spanish capital as he achieved a new feat, becoming the first player to defeat Nadal and Novak Djokovic in consecutive matches.
Record 21-time grand slam winner Nadal acknowledged that Alcaraz's meteoric rise to success has caused somewhat of a changing of the guard within Spanish tennis.
"First, I think he is young, he is new and all the new things are much more interesting than older things. Without a doubt, when you see a new car, it always looks better," Nadal said. "When you see a new phone, they always look better than the old ones. It's something that is normal in this life. I can't complain at all about that.
"At the same time, I am happy to have somebody like him from my country achieving all the things that he is achieving."
Alcaraz opted to sit out of the Internazionali d'Italia this week to recover from an ankle injury, with the upcoming French Open at Roland Garros his next target for more success.
Nadal has had his injury problems as well, only recently returning from a rib injury that kept him sidelined for six weeks, while he continues to struggle with foot issues.
"Of course, at my age, when you start having more problems than what you can manage, of course it is tough," 35- ear-old Nadal added.
"Body issues, pains, you can manage that. The problem is when you start to feel that with all the things that are going through your body, you can't be competitive enough to fight for the things that really keep exciting you."
For now, though, Nadal remains content with how he is competing as he seeks improvements in Rome, where he faces either John Isner or Francisco Cerundolo in his opening match.
"I like what I do, honestly. I am not playing anymore for things outside of my happiness and for things outside of my personal motivation," he continued.
"For the moment I am happy. It is true that I went through, again, a tough period of time. But I am here to enjoy and to give myself a chance to play well here in Rome.
"I need to keep improving. In terms of movement, in terms of being more fitter, in terms of reading again the game. In general terms, [it was] not a negative week in Madrid, even if the tournament is probably the most difficult for me."