The process, known as the democratic consent motion, was first agreed between the UK and EU in the 2020 Withdrawal Agreement to give local politicians a say in the new post-EU Exit trading rules.
The Windsor Framework arrangement was agreed between the UK and EU in 2023 and effectively keeps Northern Ireland inside the EU's single market for goods.
The Secretary of State for Northern Ireland, Hilary Benn, said the vote at Stormont marked an "important step forward" for the Windsor Framework trading arrangements.
"This democratic safeguard has provided the elected representatives of the people of Northern Ireland with a say over the trading arrangements that will apply over the next four years.
"I will now proceed as required by the law, including to commission an independent review.
"The government remains committed to implementing the Windsor Framework in good faith and protecting the UK internal market, in a way that offers stability and works for Northern Ireland, for businesses, and for traders."
Nichola Mallon, Logistics UK's Head of Trade and Devolved Policy said: “Logistics UK continues to engage with the UK government, EU and the Northern Ireland Executive to secure better trading outcomes for our members.
“The logistics industry is at the coal face and is looking to the UK and EU to accelerate efforts to secure a comprehensive agreement on agri-food products and safety and security requirements to reduce and remove barriers to trade. In the interim, we continue to press for practical interventions to improve the flow of trade from GB to NI, with a Trusted Haulier Scheme at the heart of this.
“There are immense opportunities to be had from Northern Ireland’s unique Dual Market Access. Closer cooperation between the NI Executive, UK government and EU is essential so the logistics sector and wider business community in Northern Ireland can start to see tangible benefits.”
The three unionist parties opposed extending the arrangements while Sinn Féin, Alliance and the Social Democratic and Labour Party (SDLP) were among those who voted in favour. The motion was tabled jointly by Sinn Féin, Alliance and the SDLP.