Environment Minister Mark H Durkan said the centre would be updated with the new funding.
"I very much welcome the fact that the Executive has accepted my proposal that capital funding is provided to update the facilities at Exploris and keep it open," he said.
"It is excellent news for all the supporters of Exploris, both near and far, and particularly for the people of Portaferry.
"They have fought a valiant campaign, highlighting not just the regional importance of Exploris, but have also argued that it is vital to the social and economic well being of the town."
It's not clear how long the money will keep the centre running for.
The decision came about following a massive campaign of support to keep the aquarium open.
Fury erupted over the centre's proposed closure, with fears the thousands of marine animals it cared for could be killed off if the aquarium was to close.
More than 3,000 animals are currently cared for by the Portaferry-based aquarium, as revealed by the Northern Ireland Environment Agency's most recent stock take.
Supporters from around the world joined a campaign with images from Argentina, Canada, Chile, Israel, Taiwan and the United States being posted using hashtag #explorisgoneglobal.
In March Ards Borough Council allowed another two months for Stormont to make the offer of funding to keep Exploris open – but had warned this will be the last extension.
It voted to close the Portaferry facility last September.
The announcement today came as part of Stormont's June monitoring round.
The public spending budget has been cut by £78 million - with Departments of Justice, Social Development and Employment and Learning forced to sacrifice the most money as part of across the board 2.1% reductions in running costs.
A deal between Sinn Fein and the DUP on welfare reform was delayed to later this year, with a penalty of £87 million due to be imposed by Westminster for non-compliance with the so-called bedroom tax in January.
The Historical Institutional Abuse (HIA) inquiry has received the funding it requested.
The Department of Health was criticised for its budget management by finance minister Simon Hamilton and its extra payment worth £20 million from central coffers is conditional upon improvement.
Mr Hamilton said: "The reductions that departments face in October - and must begin to plan for now - will be every bit as harsh but they are completely avoidable."
A meeting of the Executive was called to ratify the deal.