Some witnesses and TV channels reported that police also used tear gas, but police denied it.
The demonstrators had marched to the CEC building from the capital’s main Rustaveli avenue, where thousands of people held a peaceful rally.
Police said protesters tried to storm the CEC building.
“As the protesters used violent methods and did not obey the instructions of the police, the Interior Ministry used proportional force within its powers,” the ministry said in a statement.
Georgia’s ombudsman and public rights defender, Nino Lomjaria, criticised the use of water cannon.
“Using water cannon in cold weather and against peaceful protesters was not justified,” she told reporters.
Opposition leaders called on supporters to leave the scene after many protesters became soaked or injured, but said the next protest would be held on Monday.
“Our fight will be till the end. We are not scared of anything,” Nika Melia, an opposition leader, told reporters.
The opposition is demanding the resignation of the CEC chief, Tamar Zhvania, and the calling of fresh elections.
According to official results, the ruling Georgian Dream party won 48.23% of the vote, with the largest opposition party, the United National Movement (UNM), taking 27.18%.
After the result gave the ruling party the right to form a government, eight opposition parties, including the UNM, said they would boycott parliament.
The opposition accuses the ruling party and its supporters of vote buying, making threats against voters and observers and of violations during the counting process. Georgian Dream leaders have denied the accusations.
Protesters moved to the CEC building after the 8 p.m. deadline to dismiss the electoral commission head and to start talks on a fresh vote passed without a response from the government.
The economy of the South Caucasus country of 3.7 million people has been hit hard by the coronavirus outbreak. The government said on Saturday it would impose an overnight curfew from Monday between 10 p.m. and 5 a.m. in the largest cities due to a sharp rise in cases since early September. Reporting by Margarita Antidze; Editing by Mike Harrison, Nick Macfie and Daniel Wallis