The incident took place in the flood-affected town of Dhanera in Gujarat, a senior police official said, adding that the person responsible had been detained.
The Congress vice-president was earlier shown black flags by protesters while he was addressing people in Dhanera.
Rahul Gandhi held the Gujarat's ruling party BJP responsible for the incidents and wrote on Twitter: Narendra Modiji's slogans, black flags and stones are not going to make us back down. We will put our entire power behind helping the people.
He added: Who ever recognises and understands the truth need not be afraid. Mahatma Gandhi has taught us this".
Congress spokesperson Abhishek Manu Singhvi accused the BJP "goons" of carrying out the "dastardly" attack.
He said that several cars in the convoy were damaged, their window panes smashed and an official of the Special Protection Group was injured in the incident.
"All this because the Congress vice-president went to a flood affected area," he said.
Members of the Youth Congress held protests in Delhi against the attack.
Gujarat Deputy Chief Minister Nitinbhai Patel said that Rahul Gandhi was offered a bullet-proof car by the state government but he chose to travel by a normal vehicle.
"Like every visiting leader Rahul Gandhi was offered a bullet-proof car by state govt but he chose to travel by normal vehicle," ," Nitinbhai Patel said
Banaskantha Superintendent of Police Neeraj Badgujar said a man threw stones at the Congress vice president's car breaking its rear glass when he on his way from Lal Chowk to the helipad in Dhanera.
"We have detained the person who threw stones on the vehicle of Rahul Gandhi," Badgujar said.
Before the stone-pelting incident, Rahul Gandhi was heckled by protesters while he was addressing people in Lal Chowk area.
He left the stage in a huff after protesters showed black flags to him.
Some of the people gathered at the spot also raised slogans hailing Prime Minister Narendra Modi.
The Congress MLA from the area is a part of the legislators who have been flown to Bengaluru to avoid them crossing over to the BJP ahead of the August 8 Rajya Sabha polls.
Nitinbhai Patel said that people likely hurled black flags at Rahul Gandhi in protest against the Congress legislators moving to a resort in Bengaluru at a time of floods.
"We are working but Congress MLAs of the area are at a resort in Bengaluru. May be it was a protest on it," the Gujarat deputy chief minister said about the attack on Rahul Gandhi.
The Congress vice president's car was pelted with stones during his visit to a flood-affected town in Gujarat ||He was earlier shown black flags by protesters while he was addressing people in?Dhanera ||Rahul Gandhi blamed the BJP for the incidents