The fund will provide financial support and loan funding for technical, commercial, export-related and sector-specific advice for businesses. There will also be support for agriculture.
It will also be used to help employers retain and attract EU nationals to work in Wales.
Jones said: “Brexit poses different challenges and opportunities for each and every aspect of Welsh life – from our local businesses and major employers, to our farmers, hospitals and universities.
“The EU transition fund will help meet the challenges that lie ahead. My priority is to ensure Wales is in the best possible position to deal with the challenges and opportunities ahead.”