Ms Stokes, 89, would have been the oldest contestant if she had remained in the electoral fray. She represented Theog in the outgoing House.
"There were errors in Form B and (hence) her nomination was rejected," an official told IANS.
Form B is a declaration that a candidate has a particular party's mandate to contest the election.
Now, Deepak Rathore will be the Congress candidate from Theog against Bharatiya Janta Party's Rakesh Verma and Communist Party of India-Marxist's Rakesh Singha.
Ms Stokes, the Irrigation and Public Health Minister and eight-time legislator, on Monday filed her nomination from Theog in Shimla district.
Earlier, the Congress had cleared Deepak Rathore's name for Theog after a lot of deliberations on Sunday. He too filed his nomination from Theog on Monday as Stokes' covering candidate.
Ms Stokes, a long-time Indian hockey administrator and daughter-in-law of American missionary Satyanand Stokes, had earlier declined to re-contest from Theog as Chief Minister Virbhadra Singh had expressed a desire to contest the seat.
Later, the Chief Minister decided to contest from Arki in Solan district. Following this development, Ms Stokes expressed her desire to re-contest from the seat she represents.