Its ruling body voted in favour of a proposal by leader Mike Nesbitt for the party to withdraw from government.
He had made the recommendation after police in Northern Ireland said members of the Provisional IRA were involved in murdering ex-IRA man Kevin McGuigan Sr.
Mr Nesbitt said Danny Kennedy, the UUP's only executive minister, will now resign, and he described the executive as a "busted flush".
The party's leader Mike Nesbitt said Mr Kennedy would tender his resignation on Tuesday.
Mr McGuigan Sr's murder earlier this month has raised questions about the status of the political institutions in Northern Ireland.
Chief Constable George Hamilton said an infrastructure still exists at a senior level of the Provisional IRA.
But he added there was no evidence that Mr McGuigan Sr's murder was sanctioned by that hierarchy.
Sinn Féin said the Provisional IRA had "gone away" after ordering an end to its armed conflict in 2005.
Mr Nesbitt said Sinn Féin had "no credibility and we have no trust and without trust we have nothing".
The UUP's executive, which has over 100 members, met at a hotel in east Belfast to discuss Mr Nesbitt's recommendation for the party to pull out of government.
It voted unanimously to support the move.
Sinn Féin MLA Gerry Kelly said Mr Nesbitt was "trying to spook the DUP into pulling the institutions down".
"I think [he] is setting leadership aside here for narrow party political reasons, even though he argues that it's quite the opposite," Mr Kelly said.
"What unionism needs to realise if it is pulling down these institutions is that they're not just punishing the nationalist vote, they are also punishing the voters who vote for unionists."
The DUP said earlier this week it believed that if anyone was excluded from government in Northern Ireland it should be Sinn Féin, "not unionists".
The SDLP and the Alliance Party both said ahead of the meeting that a decision by the UUP to leave the executive would be "premature".
The Ulster Unionist Party (UUP) will leave the Northern Ireland Executive.