The nomination of the 89-year-old leader was rejected by SDM Tashi Sandup on the ground that another candidate Deepak Rathore had filed his nomination papers as a Congress candidate for the same seat in Shimla district ahead of Stokes, officials said.
Both Rathore and Stokes had authorization letters from the Congress, they said.
During scrutiny of nomination papers, objection was voiced regarding on Stokes' nomination and the Returning Officer gave both the candidates time till 4.00 pm today to settle the issue.
Stokes had initially decided not to contest the election for 11th time and had vacated the Theog seat for Chief Minister Virbhadra Singh.
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But Virbhadra Singh decided to contest from Arki, following which Stokes reportedly pushed the name of Vijay Pal Khachi.
The Congress high command, on its part, gave ticket to Rathore and finally she decided to enter the fray for 11th time.
Assembly polls in Himachal Pradesh will be held on November 9.
Stokes, the Irrigation and Public Health minister, is an eight-time MLA.
She lost the elections from Theog in 1977 and again in 1993 but won in 1982, 1985, 1990, 1998 and 2012 and was elected from adjoining Kumarsein constituency in 2003 and 2007.
She was Speaker of Vidhan Sabha from 1985 to 1990 and served as a minister from 2003 to 2007 and from December 2012 till date.