This was an integral part of what prosecutors once called "a mountain of evidence."
"If they're so invested that they decide to take this case to trial, I believe they're going to get their 'you know what' handed to them," BALCO founder Victor Conte said.
Conte is not surprised by the ruling. Even if the Appeals Court had ruled that the drug tests were admissible, Conte believes prosecutors still do not have the goods on Bonds.
"The blood tests and the urine tests, there are all kinds of inconsistencies there that I believe the government would have an awfully hard time connecting the dots," he said.
At the heart of Friday's ruling are three positive drug tests which prosecutors say are linked to the slugger.
They contend that in 2001, Bonds' trainer Greg Anderson administered the tests and took the samples to BALCO.
U.S. District Court Judge Susan Illston, who is presiding over the case, threw out that evidence early last year, as well as doping calendars and logs which were seized at Anderson's home.
That was because Bonds' trainer told the judge he'll refuse to testify at Bonds' perjury trial. He already served about a year in prison for contempt, after refusing to testify before the grand jury.
Illston ruled the drug tests can't be tied to Bonds without Anderson's testimony, and the appeals court agreed.
Journalist Lance Williams co-authored the book "Game of Shadows" which chronicles the Bonds steroid controversy. He says there is still one other positive drug test that baseball league officials conducted which prosecutors can admit as evidence.
"They got him on an MLB test in the year 2003 using 'the clear,' the undetectable steroid that BALCO was distributing," Williams said.
But prosecutors may still have a tough case against Bonds even with that evidence.
"His essential defense is 'Yeah, I may have very well taken steroids but I was an innocent victim. I was being given steroids and I didn't know it,'" ABC7 legal analyst Dean Johnson said.
Bonds' defense team says in a written statement to ABC7 that the court made the right decision, adding that: "Much of the evidence the government sought to introduce against Barry Bonds was unreliable here say and therefore inadmissible at his trial."
The U.S. Attorney's Office declined to comment.