However the 31 year old Nadal would close out set one on his second set point with a down the line forehand winner after 56 minutes of play.
In set two, Nadal raced to a 5-1 lead behind strong baseline play.
Nishikori then held serve to reach 5-2.
In the final game of the match with Nadal serving at 30-15, Nishikori netted a crosscourt on the run forehand to face double match point.
Nadal, who did not drop a set all week, finished the match with a crosscourt backhand winner after one hour and 33 minutes of play.
The Spaniard, known as the king of clay, won 81 matches in a row on the surface from 2005-2007.
Nadal as well is a ten time Roland Garros champion after winning last year in Paris.
Roland Garros, the second of tennis’ four grand slams, begins May 27th.
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