Opposition MPs physically tried to stop the vote in a legislative committee by jostling around the chairman and trying to snatch his paperwork and microphone.
The committee's vote clears the way for the bill to go to the upper house of parliament for final approval.
The opposition says it will continue to try to delay the vote.
The bill would allow Japan to defend its allies overseas even when it is not under attack.
The bill is not widely supported by the country at large. Thousands of protesters rallied outside the parliament in Tokyo as the committee debate was under way.
Opposition lawmakers tried to physically prevent the debate from taking place.
In rare heated scenes, jostling members of the upper house surrounded the chairman of the security committee, Yoshitada Konoike, as he opened the debate on Wednesday and again on Thursday morning as the vote was taking place.
The opposition had also tabled a no-confidence vote against Mr Konoike.
Wednesday night's session was abandoned in the early hours of Thursday after opposition lawmakers blocked entry to a room where Prime Minister Shinzo Abe and other ministers were waiting to discuss the bill.
The bill has already been approved by the government-dominated lower house.
It is expected to be passed in the upper house because the ruling coalition has a majority there - this was why opponents were keen to prevent the committee from approving the legislation.
It is thought Mr Abe's government wants to pass the bills before the country goes into a five-day holiday on Saturday, which could provide an opportunity for even bigger protests.
If the upper house does not pass the bills within 60 days, they will have to be returned the lower house.
It is a step Mr Abe is thought to be willing to take. His Liberal Democratic Party-led bloc has a two-thirds majority in the lower chamber, the House of Representatives.
Despite his majorities in both houses, the controversial bills, and Mr Abe's determination to push them through despite vocal opposition, appear to have damaged his popularity.
Polls have consistently shown a majority of the public are opposed to the changes, and relatively few strongly support them.
Japan's post-World War Two constitution bars it from using force to resolve conflicts except in cases of self-defence.
Mr Abe's government has pushed for security legislation that would allow Japan's military to mobilise overseas when these three conditions are met:
What's behind Japan's military shift?
The government says Japan needs to pass the bills, which are welcomed by the US, to ensure regional peace and security in the face of rising Chinese assertiveness. It also says they will allow the country to participate more widely in global peacekeeping missions.
But opponents say the legislation violates Japan's post-war pacifist constitution, and could lead to it being dragged into US-led conflicts.
Despite the likelihood of eventual defeat, opposition to the bills has been credited with helping reverse decades of youth disengagement from politics in Japan. Students in particular, have been closely involved in leading protests once dominated by trade unionists and greying left-wing activists.

The environmental watchdog said it received a large number of complaints to its pollution hotline after a fault caused high-pressure steam venting.
The noise stopped when the fault, which took several hours to investigate, was fixed at about 23.00.
Sepa said its inspectors would be following up the incident with Ineos.
Scott Cumming, 42, who lives in Linlithgow, about seven miles away from the site, said: "It was a bit like the noise from an aircraft landing or taking off.
"It went on for literally hours. I wrote an email to Ineos asking if they could give an explanation but I haven't had a reply from them."
A post on the Sepa Facebook page read: "We're aware of a very loud noise in Grangemouth last night, which caused significant disturbance and public complaints in the wider area.
"This was caused by high pressure steam venting from the Ineos Power Station at Grangemouth, due to a fault.
"It took a numbers of hours to investigate and correct. The noise ceased when it was corrected at 11pm.
"We'll be following the incident up with Ineos."
A controversial bill to expand the role of Japan's armed forces has cleared another hurdle in parliament, but sparked scuffles among lawmakers.
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Noise from the Ineos petrochemical site in Grangemouth caused "significant disturbance" to the public on Tuesday night, according to Sepa.