Asia's top player, the world No 6, will meet Hubert Hurkacz in the second round at the Aviation Club. The Pole beat French qualifier Corentin Moutet 6-3, 7-5.
Cilic became the highest seed to exit so far as he went down to Gael Monfils, with the Frenchman storming through a decider to win 6-3, 4-6, 6-0.
Nishikori has shaken up his schedule this season and is playing Dubai for the first time after limiting himself in the past to North American venues including the defunct Memphis event and Delray Beach at this time of year.
Victory over the unpredictable Paire took 81 minutes.
"It's never easy playing Benoit, of course. Great serve, great backhand. Tricky player. Good dropshot, good touch," said Nishikori.
"The key to the first set was the (eight-minute) long (third) game.
"After I got that one, I was more confident - but if he broke back, anything can happen.
"It was good match, it's never easy with this wind. I think played good enough tennis today."
Nishikori saved eight break points in the opening set to blunt the Frenchman's attack, with two breaks in the second set enough to ensure victory.
The top seed stands 12-2 for the season after a title in Brisbane, reaching the Australian Open quarter-finals and the semis this month in Rotterdam.
Third seed Cilic, the 2014 US Open winner, has made a slow start this season and is playing in just his second event of 2019 after a knee injury.
Monfils won the Rotterdam title this month and arrived in the emirate in full flow.
"I thought I got a bit unlucky in the draw, Marin is such a tough first round," Monfils said.
"But I was ready, I like the way I competed and played, especially how I came back after losing the second set.
"It's a daily job for me and my team to stay focused, when you are concentrating so much on your tennis, it's natural to concentrate on your job."
Monfils will play Marcos Baghdatis in the second round. The Cypriot beat Egyptian Mohamed Safwat 4-6, 6-3, 6-4.
Lithuanian qualifier Ricardas Berankis knocked out another seed after Monday's exits of Karen Khachanov and Milos Raonic, beating Russian eighth seed Daniil Medvedev 6-3, 6-3.
Two-time finalist Tomas Berdych escaped with a win over Ilya Ivashka of Belarus 6-4, 4-6, 7-6 (7/4).
American Denis Kudla eliminated Matteo Berrettini of Italy 2-6, 7-5, 7-5, while Egor Gerasimov of Belarus beat Dutchman Robin Haase 7-6 (7/2), 7-6 (7/5).