The Spaniard fired 39 winners, broke Kha nano five times and won 83 percent of his first serve points to improve to 8-0 lifetime against the Russian.
2009 champion in top form as he ousts Olympic silver medalist
Nadal jumped out to a quick 3-0 lead in just eight minutes with his serve on point and he didn't lose a point through his first three service points, the single break enough to claim the opening set.
The Spaniard broke in the opening game of the second set, his return game as sharp as ever. After being pushed to deuce, Nadal held to go in front 3-1.
A second break put the 2009 champion in complete control of the set and despite three aces for the Russian to hold, Nadal eased to a two-set lead with more splendid overall play.
Khachanov raised his level of play in the third set and he stunningly broke after trailing 40-0 in Nadal service game. He saved two break points to hold for a 4-1 lead.
Neither man had trouble holding the rest of the set and the 28th seed posted a love hold to close out the set and cut the Nadal lead to two sets to one.
The fourth set mirrored the first two, the Spaniard breaking early and going in front 2-0. A second break was achieved with more imperious groundstrokes and on match point, an ace wrapped up a masterful performance.