Novak Djokovic has struggled since returning from a layoff for a right elbow injury and is yet to reach the quarterfinals in the six tournaments he has played this year.
Djokovic lost in the third round in Monte Carlo and in the second round in both Miami and Indian Wells. The 12th-ranked Serb also failed to advance past the last 16 at the Australian Open.
Serena Williams has withdrawn from next week's Italian Open, saying she needs more time to be "100 percent ready to compete."
Top-seeded Simona Halep reached the third round by beating Elise Mertens 6-0, 6-3.
Djokovic broke serve late in each set to get past the 20th-ranked Nishikori after nearly two hours in the Magic Box.
Alexander Zverev defeated three-time former champion Philipp Kohlschreiber 6-3, 6-3 to defend his Munich Open title on Sunday.
Petra Kvitova came from a set down to beat seventh-seeded Mihaela Buzarnescu of Romania 4-6, 6-2, 6-3 in the Prague Open final.
Sania and her cricketer husband Shoaib Malik, who got married in 2010, announced her pregnancy last month.
Nadal has said that despite a torrid start to his clay-court campaign it was unlikely he would be able to overcome an injury hiatus earlier in the season.
Williams, a 23-time Grand Slam champion, returned to the tour in Indian Wells this year after a 14-month absence because of the birth of her daughter.
Nadal, who also won his 11th Monte Carlos Masters title last week, was never seriously challenged on his way to a 19th straight victory on clay.
The sixth-seeded Czech held her nerve at key times to win her first title of the season and her 10th overall in just under two hours.
The top-ranked Spaniard will now take on 19-year-old Stefanos Tsitsipas, the first Greek player to make it to an ATP Tour final in 45 years.
Nadal will next face David Goffin, who defeated Spaniard Roberto Bautista Agut 6-7 (3), 6-2, 6-2.
Nadal, coming off his 11th Monte Carlo title, has won 11 of his 12 ATP Tour matches this season, with the only loss coming from an injury retirement in the Australian Open quarterfinals.
Djokovic, trying to return to form after a lingering right elbow injury, hasn't made it past the last 16 in five tournaments this year.
On Monday, Sania and Shoaib tweeted an image on their official Twitter handles which more or less confirmed the news of the pregnancy.
Nadal also became the first male tennis player in the Open era to win the same title 11 times — 13 years after his first title here.
The top-ranked Nadal will face Kei Nishikori, who beat No. 4-ranked Alexander Zverev 3-6, 6-3, 6-4.
Djokovic was once Nadal's nemesis, even on clay. He ended the Spanish player's 46-match winning run by beating him in the 2013 final, and then won the tournament in 2015.
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