The budget will be debated in the Senedd on 3 November.
On Tuesday, First Minister Rhun ap Iorwerth said: “This agreement reflects what can be achieved when parties across the Senedd work together.”
Skates said Labour had “managed to secure a significant cash injection for schools”.
“While we still believe the Welsh government should be setting aside more for ALN in schools, it is a welcome first step in dealing with the need to better fund schools.”
Plaid Cymru’s original mini-budget included £100m for the NHS to bring down waiting times, £55m for childcare and £40m for school repairs.
If the supplementary budget is not passed then the government would have to find other ways to fund its new plans.
It was not clear if the £60m offered in the deal is annual. Education Minister Anna Brychan said allocation for future years would be part of the preparations for the draft budget for 2027-28.
Talks are ongoing with other parties for the Welsh government’s full annual spending plans, which will be voted on by the Senedd early next year.
Helen Jenner, leader of Reform Wales, said: “This deal may be good for the failed establishment of Plaid and Labour, but it does not deliver for Wales.
“While we welcome extra support for additional learning needs provision, the Welsh government is still sending millions of pounds of taxpayers’ money overseas while our public services suffer here at home.”
Former Welsh Labour leader Mark Drakeford previously said his party had made mistakes in how it handled negotiations with Plaid over the summer, and suggested there was a case to be made to take the money previously offered by Plaid.
Following Tuesday’s announcement, Llŷr Powell, Reform’s chief whip, said: “When Mark Drakeford speaks, Ken Skates starts dancing.”
It is not known yet if Labour will vote for or abstain on the budget as part of the deal, but a Labour source said the party will allow the supplementary budget to pass.
There were angry scenes in the Senedd in July when the Plaid Cymru government brought its supplementary budget to a vote without a deal in place.
Plaid failed to get any opposition support for the package.
Finance Minister Elin Jones accused Labour of behaving as a “destructive opposition” at the time.
Tory Senedd leader Darren Millar said the decision to vote on the budget anyway was “bonkers”.
The first minister later said his government had learned “lessons” from the episode, and promised to improve the way his government engaged with others.
