54-year-old Shirani Bandaranayake was served a notice ordering her to quit her post, two days after the Parliament overwhelmingly voted to impeach her deepening the row between the judiciary and the government.
Presidential aide Wijayananda Herath said the letter signed by Rajapaksa was delivered to the Chief Justice's residence.
Bandaranayake's lawyers confirmed the receipt of the letter informing her of her removal from the post.
The impeachment of Bandaranayake had earlier been ruled as unconstitutional by courts and a finding by the Parliamentary committee that held her "guilty" had been quashed.
The impeachment of the Chief Justice went ahead despite calls by rights groups, citizens, clergy and lawyers who asked the government not to do so.
By ordering the sacking of Bandaranayake, Rajapaksa acted in defiance of several international pleas for a review of the process, including from the US and UN.
The Parliamentary committee on December 8, 2012, had ruled that Bandaranayake was guilty of three of the 14 charges in the impeachment proceedings against her moved by the ruling UPFA coalition legislators.
The three charges were of financial impropriety based on non-declaration of assets and conflict of interest in a case involving a failed investment company.
Bandaranayake denied all the charges against her. On December 6, she stormed out of the impeachment hearing in Parliament, saying she would not be given a fair trial.
She also claimed that she faced verbal abuse by the government members of the Parliamentary committee.
On Friday, the Parliament voted 155 to 49 to dismiss Bandaranayake, whose recent rulings had gone against the government.
Presidential officials said that Rajapaksa would next move to appoint Bandaranayake's successor.
Bandaranayake's lawyers did not want to comment on possible future moves by her.
Her removal pushed Sri Lanka into the brink of a major Constitutional stand-off.
The Supreme Court had earlier ruled that the Parliamentary select committee which found Bandaranayake guilty was illegal. The Appeal Court later quashed findings of the select committee.
The dispute between Bandaranayake and the government flared up late last year as the Supreme Court ruled independently on some of the key decisions of the Rajapaksa administration which has tightened its grip on power after crushing the LTTE in May 2009.
Bandaranayake's husband is also the subject of an ongoing investigation by the anti-graft commission.