In an 8-2 vote --with Earl Campbell and Michael Rivers opposed and Evva Anderson absent -- the board voted to reduce the contribution from roughly $2.3 million to just under $2.1 million.
The difference of $288,770 will be used to expand career and technical programs in Beaufort County schools, according to the motion approved Thursday night.
The vote was taken publicly after a nearly two-hour discussion in executive session. Board members said they went into closed session because the subject involved "contractual matters."
"We believe our relationship with ACE is a contract and something we can discuss in executive session," board chairman Bill Evans said after the meeting. "We've talked about ACE in prior executive sessions. I think the difference is that we took some action coming out of this one ... ."
Many previous discussions about the proposed ACE budget have taken place in public session. Evans said he had no specific reason why Thursday's discussion happened behind closed doors.
He said the conversations in the closed session were "deliberate and appropriate."
"Yes, there were differences and there have been differences about this before," he said. "We also felt that we had not finalized the budget yet and needed to finalize something."
The overall budget will be presented to county council Tuesday for its first of three readings for approval.
The school board had delayed certifying it 2015 budget at its May 6 meeting and failed to agree on a spending plan at its Tuesday meeting.
The main point of contention has been how much the district should give to ACE, superintendent Jeff Moss has said.
Several board members have said not enough money was going to ACE classrooms.
However, Rivers and Campbell -- who both serve on the ACE board with fellow school board member Jim Beckert -- have said that decreasing the budget was not the way to address those concerns.
Evans said that many board members felt ACE could use money from its $431,000 reserve fund to make-up the reduction.
"My concern is that we've given ACE money overtime, and it doesn't get spent in the reserve fund," he said. "They don't need a reserve because Jasper and Beaufort counties provide support in an emergency."
Jasper County contributes a little more than $1 million to ACE annually.
Beaufort County's certified budget also includes about $10 million in increases over the current year's spending plan, largely due to unfunded state mandates and growing enrollment, according to Moss.
Follow reporter Sarah Bowman on Twitter at twitter.com/IPBG_Sarah.