Mannarino beat local hope Yuichi Sugita 6-2 6-4.
Fourth seed David Goffin stayed on track for a final showdown with Cilic after beating Richard Gasquet 7-5 6-2 in his first meeting with the Frenchman.
Goffin eliminated Cilic in the semi-finals in Tokyo last year and has three wins in five previous meetings with the world number five, including one in the Davis Cup, but faces a tricky semi-final against Argentine eighth seed Diego Schwartzman.
A strong start was enough to see Schwartzman ease past Steve Johnson in straight sets.
The American, who pulled off a big upset in the first round when he eliminated second seed Dominic Thiem, struggled with his serve and surrendered the first set without winning a game.
He finally started to find some form in the second set, but it was a case of too little too late as he bowed out 6-0 7-5.
(Writing by Simon Jennings in Bengaluru, editing by Ed Osmond)
