The bonus was introduced amid the financial crisis in 2012 as a welfare measure and work incentive, but it has grown from a few hundred recipients to almost 9,800, who receive EUR 50-200 per month.
The veto had been proposed by a group of councillors representing employees, who disagree with the government's reasoning that the abolishment of the benefit will encourage people to take a full-time job.
The group believes the measure will further push the most vulnerable workers into social distress, arguing the affected families and individuals will have less disposable income and will be thus more exposed to poverty and social exclusion.
National councillor and the head of the ZSSS trade union confederation Lidija Jerkič also rejected the government's argument that the bonus needed to be abolished because it was being abused.
"If there are really cases of abuse, the bonus should be scrapped for those abusing it and not simply for everybody," Jerkič said.
The government's position was presented by Labour Ministry State Secretary Tilen Božič, who also noted a series of measures had been adopted that would offset the scrapping of the bonus, including a substantial increase of the basic welfare allowance.
The councillors did not discuss the proposal, but some of them explained their vote, with the upper chamber's president Alojz Kovšca for instance siding with those opposing the bonus.
"In the National Council I represent the interests of craft and independent professionals – they are telling me they are unable to get workers, which is why I will not back the veto," Kovšca said.
Some councillors abstained from voting, including former People's Party (SLS) president Marko Zidanšek, who said "work has been invalidated in this country – on one side through poorly devised welfare policies and on the other side by underpaying honest work".
A vote in favour of the veto on the other hand for instance came from Zagorje ob Savi Mayor Matjaž Švagan, who is convinced the state will be able to save the EUR 16 million in costs for the bonus in another way.
The legislation had been passed in a 34:18 vote 29 October, and the government will need at least 46 votes in a revote.
Strong pressure against the scrapping of the bonus has come from NGOs and trade unions, while the bonus is also supported by the opposition Left and the junior coalition SocDems.