The 31-year-old saw off Nishikori 6-3, 6-2 to become the first man to win a single tournament 11 times in the Open era with his 76th ATP Tour title.
Nadal’s 31st Masters title is also an outright record, pulling him out of a tie with Novak Djokovic.
“We’ve had some tough moments over these last five months,” said Nadal, who was playing at his first ATP event since retiring from an Australian Open quarter-final against Marin Cilic with a hip injury in January.
“I’ll enjoy the moment and then tomorrow we’ll start to think about the next tournament. But now I’ll enjoy winning a Masters 1000 tournament which doesn’t happen every day.”
The 16-time Grand Slam champion’s era of utter dominance on clay looks unlikely to end any time soon after Nadal took his run of consecutive sets won on the surface to 36.
Nadal had to win the tournament to remain at the top of the world rankings ahead of Roger Federer, who is skipping the clay-court season, and he did just that without losing more than five games in a match.
The Spaniard will next set his sights on an 11th Barcelona Open victory next week, and it is hard to see anyone preventing him from extending his record number of 10 French Open titles at Roland Garros at the end of the clay-court season.
He was pushed by Japan’s Nishikori early on and fell a break down, but roared back against an opponent who already appeared beaten midway through the first set.
“My legs were very heavy today, playing three sets three days in a row, playing with tough players. It wasn’t easy physically, obviously,” admitted Nishikori after playing seven more sets than Nadal in the tournament.
It was still an excellent week for the former world number four, who only returned from a four-month absence with a right wrist injury in January and will rise from his current ranking of 36 to the brink of the top 20.
“Tough day today playing Rafa. He was a little too good today,” added the 28-year-old.
“But I think I’ve been playing well this week, and I think I’m almost there.”
– Nadal snuffs out early threat –
Nadal got on the board with a strong service hold, before quickly putting Nishikori under pressure as a flicked passing shot brought up break point.
But the Spaniard missed a forehand up the line by a matter of millimetres, with Nishikori clinging on after an 11-minute game that left him looking physically exhausted.
But that hold showed Nadal, who first won the event in 2005, that his opponent was up for the fight.
The top seed was even displaying rare signs of nerves, and Nishikori broke for a 2-1 lead with a backhand up the line after a Nadal double fault.
But he failed to build on that glimmer of an opening, double faulting himself on break-back point.
That costly error knocked the early aggression out of Nishikori’s groundstrokes, and Nadal sped through the next two games to take command of the first set.
Nishikori forced a break point in the seventh game but fired long with the court wide open as Nadal kept his nose in front.
He struggled a little to serve out the opener, but although Nishikori saved one set point with an exquisite backhand volley, Nadal clinched it on the second with a punch of the air celebrating a pair of blistering forehands.
Nishikori was staring down the barrel of defeat at the start of the second set, but staved off a break point to hold serve.
But the last rites had long been written, and Nadal broke to 15 in each of the Japanese’s next two service games to close on victory.
The greatest player to ever step foot on a clay court secured his 24th Masters title on the surface with a venomous backhand that flew past the hapless Nishikori.