President Kalam, who had been consulting constitutional experts on the matter, finally lent his signature to the order on Thursday evening, it is learnt.
The Election Commission had contended that Bachchan held an office of profit as chair of the Uttar Pradesh Film Development Corporation.
The Uttar Pradesh assembly had March 9 attempted to circumvent the recommendation by removing 79 posts, including Bachchan's, from the list of offices of profit. However, Governor T.V. Rajeshwar had not given his assent to this.
The Election Commission had March 6 recommended Bachchan's disqualification, even as her Samajwadi Party cried foul saying it was a "conspiracy" by the ruling Congress.
The Election Commission has also asked Samajwadi Party general secretary Amar Singh to explain why he should not lose his Rajya Sabha seat for holding an office of profit. Singh heads the Uttar Pradesh Development Council.
The Election Commission had last October issued a notice to Bachchan asking her why she should not be unseated from the Rajya Sabha. It acted after receiving a complaint from defeated Congress candidate Madan Mohan that she had accepted an office of profit after becoming an MP.
Bachchan claimed that she does not receive a salary and thus could not be said to be holding an office of profit.
"The matter may be remitted back to the Election Commission to give a proper hearing and for passing fresh orders after considering all materials," she said in a letter to the president urging a review of her case.
The actor said the Election Commission had delivered its "opinion" without examining her appointment order that was lying in a sealed cover with the Allahabad High Court, adding she had failed to get the court to reverse its order.
She has also petitioned the Supreme Court to define the term office of profit.