On Saturday, India's doubles team of Yuki Bhambri and Saketh Myneni will team up for the doubles.
Nagal was no match for World no 37 Cilic and won just one game in his entire match. Cilic ended up winning 6-0, 6-1 and the match lasted just under an hour.
Croatia's Mate Pavic and Franko Skugor will now face Leander Paes and Rohan Bopanna in the doubles before Cilic takes on Gunneswaran and Gojo clashes with Ramkumar.
Non-playing captain Rohit Rajpal, while explaining the surprise decision, said that conditions demanded that Ramkumar should play instead of Sumit Nagal.
Japan's home Davis Cup match becomes the latest sporting event in the country to be affected by the rapidly spreading coronavirus.
Earlier, Leander Paes and his partner Jelena Ostapenko were crashed out of the mixed doubles events of the Australian Open.