Hidalgo largely beat conservative candidate Rachida Dati, according to estimates based on partial results.
She is backed by the Europe Ecology-The Greens party, which gained strong influence nationwide in Sunday's voting.
The second phase, originally scheduled for March 22, was postponed after France went into lockdown.
Green politicians claimed victory in several major cities of France on Sunday, including Marseille, Lyon, Besançon, Poitiers, Strasbourg, and Bordeaux.
By 5.00 p.m. (1500 GMT) only 35 per cent of voters had cast a ballot, below the 52 per cent registered at the same time in the last municipal elections in 2014, and political observers forecast a record low.
In France's two-round electoral system, the second and final vote would normally take place a week after the first.
In the election, voter turnout was low and people wore face coverings due to the coronavirus pandemic.
In Paris incumbent Mayor Anne Hidalgo - whose Socialist party has been all but wiped out at a national level - won comfortably.
Interior Minister Christophe Castaner, in charge of organizing the elections, said that "today, everywhere across France, health measures. were able to be respected. That is a satisfaction".
Voters chose mayors and municipal councillors at polling stations operating under strict hygiene rules.
The first round of votes controversially took place just two days before President Macron declared lockdown in France in March.
The spread of the coronavirus has slowed significantly in France in recent weeks and nearly all restrictions on social and business activity have been gradually lifted over the last month. France has reported almost 200,000 confirmed cases and 29,781 deaths in the pandemic.
The polls are seen as a key political indicator ahead of the 2022 French presidential election.
His government has faced criticism during the pandemic over mask shortages, testing capacity and a lack of medical equipment.
The final round of local elections where delayed due to the coronavirus pandemic and have delivered a bad outcome for the president's party La République En Marche.
In a rare bright spot for Macron, his prime minister, Edouard Philippe, won his bid to become mayor of the northern port city of Le Havre.
Philippe has seen his popularity increase significantly in recent weeks. Although the French constitution allows Philippe to name someone to act as mayor while he remains prime minister, his win deepens questions over his job as premier.
Recent opinion polls show Mr. Macron's popularity rating is hovering around 40%, which is higher than from before the virus outbreak. The party, Republic on the Move, doesn't have candidates in every race and in some instances is backing candidates from both the left and the right instead.
A government reshuffle is expected to be carried out by Mr Macron in the wake of Sunday's result.
The conservative Republicans party, which was the big victor in the 2014 municipal election, is expected to do well again based on its strong network of elected officials.