In another upset, Karthik Kumar Pradeep rated 2004, managed to beat GM Himanshu Sharma, rated 2470.
Naiditsch, rated 2701, had a very easy outing after his opponent Varshini V, rated 2062, failed to create any chance.
"I am wary of the Indian youngsters as they are known to be dangerous and underrated. Today, it was an easy day," said Naiditsch.
Arjuna awardee GM Abhijeet Gupta rated 2610 also had an easy day in office as he beat Karnataka's Likhit Chilukuri with black pieces.