Nadal, regarded as one of the greatest clay players of all time and a seven-times French Open champion, threatened to boycott the tournament if the experiment was not abandoned after he was beaten in the third round by Spanish compatriot Fernando Verdasco last year.
Nadal, world number one Novak Djokovic and others said the blue courts, which organisers argued made it easier for TV viewers to follow the balls, were too slippery, although it was unclear whether that had anything to do with the colour.
All the courts, including the Manolo Santana show court in the futuristic Magic Box arena, have been completely rebuilt and Nadal and Djokovic, as well as Roger Federer and Andy Murray, all praised the decision on Saturday.
"The courts this year fortunately are really good," Nadal told a news conference.
"The only thing I can say is thank you to the tournament, you know, for the money that they have invested to have the highest quality courts in here," he added.
"I think that obviously the court last year was not up to the level that we needed.
"In Madrid, we have the problem of the dry climate, so it's very difficult to have the clay that settles down properly, a clay that's the same as in other places.
"The courts cannot be better. So I think from the side of the players we can only say thank you. I think that the audience will also say thank you for that."
Djokovic told a separate news conference he had yet to try out the centre court but the practice court he had used was "great".
"But also from the opinions of the other players I can hear only positive comments, so it's great to see that," Djokovic said.
"You know, of course from players' perspective it's always positive to see a tournament is doing everything they can to make a player feel comfortable playing on the court, and of course feeling good off the court as well."
Murray, who missed last year's Madrid Open through injury, added: "The courts are fantastic. They're excellent."
Federer, who did not appear too bothered by the blue clay last year as he cruised to a third Madrid title, said he had yet to try out the new courts but had heard good things from the other players.
"There was a lot of criticism about the colour, about the quality of the court as well, being extremely slippery," he said.
"I don't know if that was due to the colour, but this tournament has, in the past, had issues with the quality of the court.
"I think this year, from what I'm hearing from the players, it's a good quality court and the players are happy. In the process, hopefully we'll see better tennis this year."