An eight-year-old and a one-year-old were taken from their West Midlands home and detained for 57 days at Yarl's Wood Immigration Removal Centre with their mother and father in 2006.
The Home Office has agreed to pay £45,000 damages to the older girl and £19,500 to the younger, with the parents receiving £39,000 and £46,000.
Aynsley-Green said: "This is a good judgement. I am particularly pleased that the two children have also been awarded compensation by the court. It goes some way to righting this wrong."
The commissioner said his office was working with the UK Borders Agency to secure alternatives to detention and improvements to the asylum and immigration system for children. He said he would shortly publish recommendations and an action plan.
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