The gutted Spaniard was forced to retire with a hip problem early in the fifth set of his Australian Open quarter-final against sixth seed Marin Cilic on Tuesday.
It deprived the opening Grand Slam of the year of a potential rematch of the vintage 2017 final where Federer beat Nadal in a heart-stopping five-setter.
Federer said it hard to see Nadal's campaign end that way and the last thing he did before falling asleep on Tuesday evening ahead of his own quarter-final against Tomas Berdych was reach out to his friend.
"I wrote Rafa late last night (Tuesday) before I went to bed. Last thing I did. I said I have to write Rafa and see how he's doing.
"I was hoping he was going to be OK with the scan, hoping the news was not terrible.
"It was not nice to see a fellow rival and friend like this go out. Wish him well," he added of the 16-time Grand Slam champion.
Fortunately for Nadal, a scan showed only a torn inner hip muscle and not something more serious, and he is expected to be back in action in three to four weeks.
"I got one note from a player in the hospital when I broke my neck. Roger Federer. Tennis is lucky to have such an amazing ambassador for the game," the American tweeted.
Federer plays fast-rising South Korean Chung Hyeon on Friday for a place in the Melbourne Park final as he chases a 20th Grand Slam title.
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