Karnataka Legislative Assembly Secretary P Omprakasha, who is also the returning officer for the election, told PTI that he had passed an order to this effect.
Though Puttaswamy, who was political secretary to the chief minister, had resigned from the post two days ago, it was accepted only today, thereby attracting the office of profit clause.
Following the rejection of Puttaswamy's nomination, four candidates have been left in fray, which would ensure their election unopposed to the four Rajya Sabha seats from Karnataka.
Thursday is the last date for withdrawal of nominations.
Basavaraj Patil Sedam, R Ramakrisna (both BJP), K Rahman Khan of the Congress and industrialist Rajiv Chandrashekhar, contesting as an independent, are in the fray now.
Meanwhile, Puttaswamy claimed that he had withdrawn his nomination papers.
The BJP suspended Puttaswamy, a Yeddyurappa loyalist, from the party for 'anti-party activity' after he filed his papers.