Pentland - JD's biggest shareholder with brands including Ellesse and Mitre - will take on Canterbury's £22.7 million debt in its purchase of the firm, which also supplies the South Africa and Scotland teams.
Canterbury outgunned England's long-time supplier Nike to win the Rugby Football Union contract, which will run for four years from September.
Strong sales in New Zealand and Australia during the Rugby World Cup recently helped Canterbury to annual operating profits of £400,000, but it was dragged to a bottom-line loss by fashionwear in the US and Europe.
It has taken steps to address the poor performing areas but with JD only selling a small proportion of Canterbury's products in its stores the UK retailer said the brand was not a key part of its offer.
JD acquired its initial interest in Canterbury in August 2009 following the acquisition of the European assets from administrators, as well as rights to brands Canterbury and Canterbury of New Zealand.
Pentland, which was founded in Liverpool in the 1930s, owns a 57% stake in JD Sports Fashion and includes the brands Brasher and Berghaus in its portfolio.
In a separate deal, which is also subject to the approval of JD shareholders, Pentland has agreed to sell the casual clothing and footwear brand ONETrueSaxon to JD for £50,000.