The drama - created by Russell T Davies and Phil Ford - follows the young wizard Tom Clarke, played by Scott Haran, and his scientific friend Benny Sherwood, portrayed by Percelle Ascott, as they try to stop the Nekross, who are threatening to destroy all of wizardkind - and the Earth - in their pursuit of magic.
It will start production next month to air in 2014/15, said the BBC, which added:
The series is vivid and brave and our audience loves the portrayal of loyal friendship alongside exciting alien battles and stunning wizardry.
Children want to talk about Tom, Benny and the Nekross and we know they'll be delighted to hear a third series is being conjured up by the talented team in Wales.
Produced by BBC Cymru Wales, it is filmed at the BBC's Roath Lock Studios in Cardiff and on location around the area. Series three will be executive-produced by Ford and Nikki Wilson for BBC Wales and Sue Nott for CBBC.
UPDATE - 5th MARCH: The BBC told News In Time And Space today that the third series would comprise 10 episodes. This will make it the shortest series so far.