The verdict came after a 12-day trial and almost four full days of deliberation. U.S. District Judge Susan Illston declared a mistrial on the three counts of lying to a grand jury in 2003.
It's a messy end to a case that put the seven-time MVP - and baseball itself - under a cloud of suspicion for more than three years.
Bonds sat stone-faced while the verdict was read, while his legal team immediately asked that the guilty verdict be thrown out.
The judge did not rule on the request and instead scheduled a hearing for May 20 in the case.
"It was certainly a seriously-contested trial, and here we are. Counts one, two and three, there is no verdict, there is no judgment," said Bond's attorney, Allen Ruby, at a press conference after the verdict was read.
"The counts that allege steroids, which allege needles, which allege human growth hormone, those were mistried," Ruby said. "There was no conviction, no verdict, no finding adverse to Barry Bonds."
Ruby instructed his client not to comment since the case isn't over.
Bonds acknowledged fans outside the courthouse.
When asked if he was celebrating Wednesday night, he said, "No, there's really nothing to celebrate."
Bonds' case is the culmination of a federal investigation that began in 2002 into the Bay Area Laboratory Co-Operative (BALCO), which distributed performance-enhancing drugs to athletes.
Each count Bonds was tried on carries a maximum sentence of 10 years in prison. However, federal guidelines suggest a total sentence of 15 to 21 months.
One juror said he's glad the trial happened because it brought out Major League Baseball's dirty secret.
"All the players that testified on the stand and came clean are the true heroes," said the juror only identified as Steve."They finally said, 'Yeah, we've been taking steroids all along. Now we're coming clean. We're telling it the way it is.' I believe there's one man that couldn't do it because of who he is."
The Associated Press contributed to this story.