The billionaire tycoon’s populist movement ANO won 29.6 per cent of the vote, nearly three times as much as the closest competitor in the election on Friday and Saturday.
Mr Babiš has vowed to run the Czech Republic like a “family firm” and has been compared to US President Donald Trump due to his business background and anti-establishment message.
His election came as a blow to the EU because he railed against EU migration policy and spoke out against joining the euro during the campaign.
There are fears that the Czech Republic could join two other rebellious Central European countries – Hungary and Poland – on a collision course with the bloc.
But Mr Babiš insisted that his party was pro-European despite reservations about talk of a two-speed Europe that could sideline countries that do not have the euro.
“It is not true that we are any threat. We are pro-European!” Mr Babis said on Saturday. “I am ready to fight for our interests in Brussels.”
The former finance minister vowed to fight against political corruption despite facing fraud charges himself.
The billionaire denies charges that he illegally received a two million euro EU subsidy when he ran his food, agriculture and chemical empire before entering politics.
He has also fought back against rivals questioning his past business practices and accusations of conflicts of interest.
The controversial Czech President Milos Zeman has said he intends to name his ally Mr Babiš as the next Prime Minister of the Czech Republic.
The election saw a record nine parties secure seats in parliament’s lower house. But Mr Babiš he could still struggle to find willing coalition partners.
The ANO’s former partners the Social Democrats and centrist Christian Democrats both said on Saturday they could not be in a cabinet with anyone under police investigation.
The runner-up centre-right Civic Democrats also ruled out a government with ANO as well as two other small factions.
Earlier this year Mr Babis put his holdings – including interests in national newspapers and a radio station – in a blind trust.