Wales first minister Rhodri Morgan said he appointed Jones on the strength of his entrepreneurial record. In the 1980s, Jones founded Penn Pharmaceuticals and Lansdales Pharmacies.
Morgan said: "Jones is one of Wales' most successful entrepreneurs with a very strong commitment to science, education and the environment.
"These strengths will be invaluable during his term of office at the Welsh Development Agency as our future economic success will be based on innovation, entrepreneurship and the knowledge economy."
Jones, 58, has been put on a three-year contract.
Rowe-Beddoe has held the £80,000-a-year post for the past nine years. He is also credited with saving the beleaguered £92m Wales Millennium Centre project after taking over its chairmanship in March.
Before his arrival, the Welsh Assembly was convinced that the millennium centre would spiral over budget, and it even considered shelving the Cardiff cultural venue.
