A bench of Justice B.S.Chauhan and Justice A.K.Sikri, while declining to entertain the plea by woman advocate Lilli Thomas, said that it was too late.
Though advocate Thomas named only Modi but Aam Admi Party chief and candidate Arvind Kejriwal too falls in the same category.
Besides Varanasi, Modi is also contesting from Vadodara Lok Sabha seat in Gujarat.
In the Varanasi Lok Sabha constituency which saw polling on May 12, Modi faces Kejriwal and Congress' Ajai Rai, who is however a local resident of the Hindu holy city.
The apex court is already seized of a petition seeking direction that no candidate could simultaneously contest election from more than one constituency in the same election.
It had March 14 issued notice to the central government and the Election Commission on a petition seeking direction that no candidate could simultaneously contest election from more than one constituency for the same legislative body in the same election.
The petitioner, advocate H.K.Naik, had contended that the founding fathers of the constitution during debates in the constituent assembly never dreamt of a scenario that one day a candidate would be filing nomination papers for more than one seat in the same election and for the same legislature.
He had sought a declaration that section 70 of the Representation of People Act, 1951, deals with the situation of a candidate getting elected from more than one seat, be declared ultra vires of the constitution.
Section 70 provides that if a person is elected to more than one seat in either house of parliament or in the house or either house of a state legislature, he/she will resign from all but one seat, and if doesn't within the prescribed time then all seats he has been elected from would stand vacated.