Lawmakers threw out the equality amendment to the bill in a secret vote, requested by a cross-party group of MPs, Il Sole 24 Ore reported.
The decision was met with disappointment by Laura Boldrini, the lower house speaker, who took to Twitter to express her “deep bitterness for the lost opportunity to the detriment of the country and of democracy.”
While the vote can be seen as a blow to the new premier’s equality drive - half of his new ministers are women - reaching a consensus on the so-called “pink quota” paves the way for an overall agreement on the new electoral law.
MPs must now vote on the proposed law as a whole, before it is passed to the Italian Senate.
Reform of Italy’s electoral law is the first challenge faced by Renzi, the 39-year-old prime minister who took the reins from Enrico Letta last month.
Renzi drew up his proposals for a new law, in consultation with political rival Silvio Berlusconi, in January after being elected leader of the Democratic Party (PD).
The current legislation - nicknamed the “pigsty” law - is widely criticized as it resulted in no clear winner following last year’s national election.
Getting Italian MPs to agree on the new bill would be the first great success of Renzi’s premiership, boosting confidence in the young prime minister’s ambitious reform programme.