This paves way for implementation of the motion, favoured by 14 of the 18 directors of GCMMF on December 5.
GCMMF sells its products under the famous Amul brand.
On Monday, a high court judge allowed the federation to implement the no-confidence motion passed against Chaudhary after January 11.
He filed appeal before the division bench, but one of the judges recused himself, so the matter got adjourned.
In October 2013, 14 member unions of the GCMMF board had moved a no-confidence motion against Chaudhary, elected as chairman in August 2012, alleging mismanagement.
Established in 1973, GCMMF is India's largest food product marketing organisation which clocked an annual turnover of USD 2.54 billion in 2012-13.