The Lagan Valley MLA opposed them over a DUP amendment to a UUP motion calling for the Assembly's commitment to inclusivity, mutual respect, peace and democracy, in the wake of the recent unrest over flags in Northern Ireland.
The DUP wanted to remove a reference to the Good Friday Agreement.
Mr McCrea said: "In his opening remarks Mike Nesbitt declared that he was 'puzzled' about the opposition to the DUP amendment and later that 'he/we would not die in a ditch' for the part of his motion that called on all parties to support the spirit of the Belfast Agreement.
"I cannot support this position. I will not accept that the Belfast Agreement can be so easily discarded and I refuse to accept that the DUP amendment is anything other than an attack on the Belfast Agreement."
Mr McCrea recently had the UUP whip removed after he spoke out of line with the party's stance on flying the Union flag at Belfast City Hall.
He agreed with the Alliance Party motion of flying the flag on designated days, and said he felt his stance was in accordance with UUP policy. He is currently facing disciplinary action.
Mr McCrea has also stated he will quit the party if an electoral alliance is formed with the DUP.
He tweeted: "I will not stand with the party if there are electoral pacts with the DUP. Unionist unity is not a good thing for Northern Ireland."
The motion condemning violence was backed by the Assembly on Monday while the amendment was not.
UUP leader Mike Nesbitt said Mr McCrea's comments were "unfounded".
He continued: "I also note the concerns expressed in the media by Basil McCrea over the Party moving away the Belfast Agreement were, therefore, unfounded.
"Indeed, it should have been clear to him that the DUP amendment was never going to pass, so there was no threat to our commitment to promoting the spirit of the Belfast Agreement.
"I am disappointed that the entire House did not support our motion, indeed some Unionists even voted against it. For those accusing me of sleeping-walking into unionist unity; look at the vote. We voted 'yes', the DUP voted 'no'.
"I remain committed to advancing the cause of the Union. Where that is best achieved by us working alone, in opposition to other unionist parties, that is what we will do, as we did today. When co-operation is called for, as it is in dealing with the street protests and their underlying issues, I shall co-operate. I continue to consult widely and continually on this strategy and am grateful for the overwhelming support of the Party."