The move, using the so-called article 49:3 of the constitution, will ensure the bill raising the retirement age by two years to 64 is adopted after weeks of protests and fractious debate.
But it also shows President Emmanuel Macron and his government failed to garner enough of a majority in parliament.
Borne was greeted by boos as she arrived in the National Assembly, the lower house of parliament, to announce the special procedure on Thursday. The session was suspended for two minutes after left-wing lawmakers singing the national anthem prevented Borne from speaking. Some brandished placards reading "No to 64 years".
When the session resumed, Borne took the floor but her speech was largely drowned out by boos and chants from opposition members of parliament and shouts of "resignation," in a rare chaotic scene in the French parliament.
"We cannot gamble on the future of our pensions, this reform is necessary," Borne told lawmakers, to explain why she was using the 49:3 procedure.
Far-right leader Marine Le Pen said Borne should resign. "This last-minute resort to 49:3 is an extraordinary sign of weakness," she said, adding, speaking of Borne: "She must go."
The Senate, upper house, had given its green light to the bill in the morning, as expected, thanks to support from senators from the conservative Les Republicains (LR).
But the afternoon vote in the National Assembly would have been a different matter. There, LR lawmakers were split on the issue and the government, which needed their support, decided at the last minute to skip a vote.
Resorting to the measure is likely to further enrage unions, protesters and left-wing opposition parties that say the pension overhaul is unfair and unnecessary.
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