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Spaniard Nadal, who fell in the third round and will lose his number two ranking to his great Swiss rival, was one of the most vocal opponents of the new surface, which he said was dangerously slippery.
Federer, however, proved better able to adapt to the testing conditions and secured his fourth title of the season, and the 74th of his illustrious career, after edging a gripping final at the futuristic Magic Box arena.
"It feels amazing," Federer told spectators sweltering in the Madrid heat inside the Manolo Santana show court as his wife and twin daughters looked on.
"Look, it's been a tough tournament and tough to move but you just go on with it and try to make the best out of it," added the 30-year-old.
"There was some good tennis and there was some bad tennis as well, you see that in all the tournaments, but I thought the level of play under the circumstances was very good."
Federer came into the tournament following a month-long rest and is looking in ominous form as the world's top players prepare for the French Open starting in Paris later this month.
The 2009 Roland Garros champion had already won titles this year in Rotterdam, Dubai and Indian Wells and has only lost three times since falling to Djokovic in the U.S. Open semi finals last September.
Czech sixth seed Berdych, who ended Federer's dream of Olympic gold in Athens in 2004 and knocked him out of Wimbledon in the quarter-finals two years ago, made the stronger start and a break of his opponent's serve in the second game was enough to settle an otherwise desperately tight first set.
The crowd, including American actor Will Smith, tried their best to lift the hugely-popular Federer, champion in 2006 and 2009, and he responded with two breaks in the second set that helped him level the match.
A couple of double faults from Berdych, who was bidding for a second career Masters triumph, put Federer 5-3 ahead in the decider but the 16-times grand slam champion faltered when serving for the match.
However, with Berdych needing to hold to stay in contention at 6-5 down, Federer conjured another break, converting his fourth match point when Berdych netted a forehand.
The statistics show how evenly matched the pair were, with Federer hitting 44 winners to Berdych's 42 and the Czech making 27 unforced errors to Federer's 30. The Swiss won 103 points to his opponent's 101.
Nadal and world Novak Djokovic have both have threatened not to return next year unless the traditional red dirt used at most other clay events is reinstated.
Organisers argue that the blue courts make it easier for television viewers to follow the yellow balls but the players' complaints may prompt the ATP, the governing body of men's tennis, to switch back to red clay next year.