Ahsan said that Musharraf's prime concern was not to properly investigate the charges that led to Chaudhry's suspension on March 9, "but just to remove the chief justice from his office".
"This is the personal malice I'm alleging," he told the court. "The malice is of the president."
The Supreme Court is hearing a petition, brought by Chaudhry, that challenges his suspension by Musharraf.
Separate proceedings by the Supreme Judicial Council on whether the judge should be sacked over his alleged misconduct or reinstated have been suspended until the Supreme Court decides on Chaudhry's petition.
'Pressured to resign'
Ahsan filed a written affidavit in which Chaudhry described his March 9 meeting with the president, saying Musharraf and the bosses of his intelligence services pressured him to resign over allegations that he secured cars for his family from the Supreme Court.
"It would be in the best interests of Pakistan for Musharraf to step down"
Jim ibarra, Cyberjaya, Malaysia
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Chaudhry was quoted as saying he rejected Musharraf's offers of another job and told him: "I wouldn't resign ... I am innocent."
The ousted judge said he was detained for more than five hours at Musharraf's office and was allowed to go home only after an acting chief justice was sworn in.
He said that as he left Musharraf's office, a military intelligence chief, who was not identified by name, told him: "This is a bad day, now you are taking a separate way."
Chaudhry also said he believes his official residence in Islamabad had been "bugged".
In another development, three Pakistani journalists working for foreign news organisations in Karachi found bullets placed in their cars in what a local media body described on Wednesday as an attempt to intimidate the press into silence.
Mazhar Abbas, secretary-general of the Pakistan Federal Union of Journalists, said: "It is very threatening. This is a serious issue. It is an attempt to gag the press, but we will not compromise on our objectivity."
An envelope containing a bullet was taped to the windscreens of vehicles belonging two journalists, while a similar envelope was thrown inside the car of a third late on Tuesday.
Karachi has been tense since May 12, when nearly 40 people were killed in clashes between rival political groups that disrupted a visit to the city by Chaudhry.
The Muttahida Qaumi Movement (MQM), an ally of Musharraf's and member of the coalition, has denied accusations that its workers played a big part in the Karachi bloodshed.
Last week, a group associated with MQM issued a list of a dozen journalists, terming them "enemies".
Two of the journalists who received bullets were on the list.