The European Commission has approved government proposals for spending the money, which is expected to create more than 150,000 new jobs and train 420,000 workers.
Merseyside, Cornwall and the Isles of Scilly, South Yorkshire and West Wales and the Valleys will benefit from the funding.
The cash is aimed at enhancing the competitiveness of the European Union's deprived regions.
The issue was crucial in toppling his predecessor, Alun Michael, who was accused of not doing enough to secure EU funds.
Mr Morgan said: 'This latest news is a vindication of all our hard work and yet another important achievement for the assembly.'