The Bill was introduced by Karen Gillon, convener of the parliamentary education committee which is initiating it rather than the Executive, one of the Scottish Parliament's powers which distinguishes it from Westminster.
Scotland now follows Wales where a commissioner already exists, Northern Ireland where a Bill exists and 18 other countries.
Ms Gillon made clear the intention was to have "a persuasive voice, a children's champion - and not an alternative to the courts". The commissioner's role will be to ensure that existing organisations work better for children.
The commissioner will have powers of investigation into whether services have acted in the interests of children, but will not be allowed to probe cases which only concern an individual child. There will be no sanctions available to the commissioner but issues can be raised with Parliament.
Since the legislation emanated from a parliamentary committee, the commissioner will be accountable to and can be removed by the Parliament. But Ms Gillon insisted that the post would be fully independent.
"By supporting the establishment of a commissioner for children and young people, we send a message as a Parliament that we are committed to ensuring the highest regard for children's rights," she said.
Ms Gillon was strongly supported by Irene McGugan, the SNP's deputy education spokesperson, who pronounced the Bill "immensely satisfying".