Prosecutors originally accused Bonds of lying 19 different times during his grand jury appearance, and charged him with four counts of perjury and one count of obstruction of justice.
Illston agreed with Bonds' attorney Dennis Riordan that prosecutors must edit out many of the alleged lies or seek a new indictment, which could contain more charges.
Prosecutors are expected to decide whether to seek a new indictment before Bonds' next court date March 21. They declined comment outside court.
Bonds' 2003 grand jury testimony was extensively reported on by the San Francisco Chronicle in December 2004 and in the 2006 book "Game of Shadows," written by the reporters from the original newspaper account. However, Friday was the first time the entire 149-page document was released.
Although the indictment last fall discussed a November 2000 test that showed elevated testosterone and the Chronicle reporters wrote about a November 2001 test that showed an acceptable level, the transcript revealed another sample that previously had not received attention.
A document labeled "BB" with Bonds' date of birth refers to a sample taken in January 2001 for testing by the Bay Area Laboratory Co-Operative, known as BALCO, according to federal prosecutors who questioned Bonds during his three-hour grand jury appearance.
BALCO was the center of a performance-enhancing drug ring. Bonds' personal trainer Greg Anderson, founder Victor Conte and three others pleaded guilty to steroids distribution charges.
In his appearance before the grand jury, Bonds said he didn't understand the results from the January 2001 test prosecutors showed him and then said "that some people may have more testosterone levels than others."
The Chronicle obtained the transcripts from lawyer Troy Ellerman, who was sentenced to two years in prison after he was unmasked as the newspaper's confidential source.
The transcript could bolster each sides' case. In parts, Bonds flatly denies ever taking steroids or human growth hormone, which prosecutors allege are lies.
During the grand jury testimony, prosecutor Jeff Nedrow confronted the slugger with "doping calendars" bearing Bonds' initials and other evidence: "Now, with what you've seen today, do you feel comfortable as you sit here today saying that you have never taken steroids?"
Bonds replied: "I feel very comfortable, very comfortable."
However, in other parts of Bonds' testimony, Bonds hedged and said he became suspicious of some of the creams and oils Anderson had provided to him.
Bonds testified he became suspicious after Anderson's house was raided that his childhood friend might have been providing him with steroids masquerading as flax seed oil and arthritis cream.
Bonds said he never asked Anderson what he was taking because he trusted the trainer. He also said he didn't ask Anderson about his relationship with BALCO.
Anderson was released from prison after spending a year locked up for refusing to testify about his relationship with Bonds. Anderson is expected to be called to testify if Bonds' case goes to trial. Anderson maintains he will refuse to testify if ordered, meaning he could return to prison.
Bonds said he doesn't pry into anyone's life, including that of his wife.
"I've been married to a woman five years, known her for 17 years, and I don't even know what's in her purse," he testified. "I never looked in it in my lifetime."
Bonds' lead attorney Allen Ruby declined comment Friday. The former San Francisco Giants star, who remains an unsigned free agent, was not required to attend the hearing and has been excused from the next court date, too.
The indictment, unsealed last November, quotes Bonds denying Anderson ever injected him with steroids, which prosecutors alleged was a lie.
Bonds was charged 100 days after breaking Hank Aaron's career home run record.