Federer and his fellow Swiss Stanislas Wawrinka were edged out by Nadal and former French Open champion Carlos Moya 6-4 7-6.
The defeat was Federer's third to Nadal in less than a month, having already been beaten in the final of the Monte Carlo Masters and then again in an exhibition match on a half-clay half-grass court in Mallorca.
Nadal and Federer had only met once previously in doubles -- at Indian Wells in 2004, when Nadal and Tommy Robredo knocked out Federer and Yves Allegro.
World number two Nadal denied his latest win would give him any advantage over world number one Federer in the singles competition this week.
''We are in the second round of the doubles. That's it,'' he said.
Federer also played down the significance of the result.
''Other people always consider Nadal versus Federer to be a singles match, but I don't,'' he said.
''I was doing this to help Stan, who has been coming back from injury. We'd been talking about it for over a year, so I thought it would be a good idea.'' REUTERS SAM RK2224