In his new role, Thomas will take charge of Emap's three advertising festivals - the Cannes Lions, the Eurobest and the Dubai Lynx.
Thomas, 45, was most recently the managing director of Emap Media, where he ran titles including Shots, Screen International and Broadcast. He was previously the managing director of Emap Australia and FHM Worldwide.
He succeeds Penny Reid, who left the festival in July for personal reasons. He will work alongside the festival's executive chairman, Terry Savage, who held the position of chief executive before Reid's appointment, and starts in his new position on 1 November.
Lowery was previously the operations director at the Cannes Lions after promotion from head of entries in 2004. She takes up her new position with immediate effect.
Thomas said: "Between now and next year's Cannes festival, I will be working closely with the team helping to make Cannes Lions 2007 the best yet, while learning about the complexities of running and staging the event. It's a huge challenge, which I relish."
Savage said: "I am pleased to welcome Phil to this important role, which will see him working alongside me in developing Cannes, Eurobest and our recently announced award, the Dubai Lynx."