Saina bagged the first game against Goto 21-13 and was leading 1-0 in the second when the Japanese retired from the match giving the world number seven Indian the win.
However, the other members of the Indian team squandered the early advantage and lost all the remaining matches.
Aparna Balan and Shruti Kurian were beaten 18-21 21-17 14-21 by the Japanese pair of Mami Naito and Shizuka Matsuo in the second match, while national champion Trupti Murgunde was drubbed 16-21 19-21 by Sayaka Sato in the next clash.
India's top doubles pair of Jwala Gutta and Ashwini Ponnappa also failed to live upto expectations as Japan widened the gap with Miyuki Maeda and Satoko Suetsuna handing them a 21-13 13-21 21-12 defeat.
Eriko Hirose drubbed India's Gayatri Vartak 21-12 21-7 in the fifth match to round off a comfortable win.
Indian women had beaten formidable Hong Kong 3-2 yesterday.