The 69-year-old party general secretary was accompanied by Leader of Opposition in Gujarat Assembly Shankersinh Vaghela, state Congress chief Arjun Modhwadiya and others when he filed his papers before the district electoral officer.
Modi, who is also contesting from Varanasi, is expected to file nomination here on the last day, April 9, for the April 30 poll.
Mistry said he had studied at the local MS University, and people of the city would embrace him.
He said he would "expose Modi's so-called Gujarat development model".
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The Congress leader was on Thursday arrested along with his supporters for tearing down Modi's posters and his party had complained to the Election Commission that the Gujarat Chief Minister was monopolising advertisement space in Vadodara by "abusing" his authority.
They were later released on personal bonds of Rs 5000 each.
District Collector Vinod Rao said that apart from Mistry, Narendra Rawat, city Congress chief, filed a nomination as a dummy candidate.
The Congress leader said that he will be "grateful" if Priyanka Gandhi visits his constituency Vadodara where he is taking on Narendra Modi.
"I will be very happy if she comes.... I will indeed be grateful if she comes for a roadshow," Mistry told PTI.
His remarks came close on the heels of reports quoting Gandhi family friend and key Congress strategist Sam Pitroda that Priyanka will share her brother and Congress Vice President Rahul Gandhi's burden.
She will interact with media more and also campaign aggressively in the coming days, Pitroda has said, making it clear that the 42-year-old would complement her elder brother's efforts, not overshadow them.
"I am full of confidence that I will turn the tables," he said.