Judge Susan Cobb approved the request by Hartford State's Attorney Gail Hardy in a ruling filed Monday.
The fire in the big top of the Ringling Brothers and Barnum and Bailey Circus on July 6, 1944, killed 168 people and injured 682 others.
Chief Medical Examiner James Gill will compare DNA samples from the remains of the two women to a sample from the granddaughter of Grace Fifield, of Newport, Vermont, who attended the circus and was never seen again.
“With DNA testing, which was not available back in 1944, there’s a reasonable possibility that we could get DNA to do testing and make a comparison and make a positive identification,” Gill told NBC Connecticut last month after testifying at superior court.
It's not clear when the exhumations at the Northwood Cemetery in Windsor will occur.