The former law professor, who stepped down as prime minister in January, was tapped for the job months ago but in-fighting led to delays in holding a formal membership vote.
An online poll, in which Conte was the only candidate, confirmed him overnight as leader with almost 93 percent, with more than 62,000 votes.
Conte promised to continue supporting Mario Draghi, who took over in February at the head of a national unity government tasked with guiding Italy out of the devastation of the coronavirus pandemic.
He told Il Fatto Quotidiano newspaper that the party would “all work to offer loyal cooperation to the government of a country that has yet to emerge from a health emergency”.
Conte was prime minister at the helm of two M5S-led governments but was never actually elected.
He was brought in after the M5S’s stunning win in elections in 2018, when the then proudly anti-establishment party won 33 percent of the vote and was propelled to power.
Founded by comedian Beppe Grillo, M5S swept up voters outraged at the austerity imposed in the wake of the eurozone debt crisis of 2011-12, which pushed Italy to the brink of insolvency.
But it fell short of the majority needed to govern, and formed a populist, eurosceptic government with the anti-immigration far-right League.
Barely a year later, it switched to a pro-European coalition with the centre-left Democratic Party (PD).
It remains part of Draghi’s government and the largest party in parliament, but swathes of its lawmakers have left or have been expelled from its ranks, and it is polling at around 16 percent.
Conte promised to make his mark in the government, which comprises most of the main political parties, saying: “We will make ourselves heard with a firm and clear voice.”