Mr Towler becomes the second commissioner in Wales's history and replaces Peter Clarke, who died from cancer at the age of 58 in January. He should start work in March.
As a former director of crime reduction for the rehabilitation body Nacro, Mr Towler has strong views on the trend to "demonise" young people. He has made calls for earlier intervention to prevent the young offending.
Since Mr Clarke's death, the post has been filled in an acting capacity from the headquarters in Swansea.
Mr Towler will be tasked with carrying on much of the office's ground-breaking work, including an anti-bullying campaign, setting up a national counselling service for children in Wales and even the state of school toilets.
Mr Towler said on his appointment: "I am looking forward to the challenges the role will bring, and also the rewards of ensuring that children and young people have a dedicated representative in Wales."