The defense rested without calling a single witness, which means the slugger will not take the stand in his own defense.
The jury of eight-women and four men was sent home and ordered to return Thursday to begin deliberations after hearing closing arguments and instructions from the judge.
Prosecutors made the request to drop one charge after it became clear U.S. District Judge Susan Illston was going to rule that they failed to prove a count that charged the home run king with lying when he denied his personal trainer, Greg Anderson, induced him "to take anything before the 2003 season."
Prosecutors argued that charge meant that Bonds would be guilty if found to take have knowingly taken any steroid prior to 2003. But the judge disagreed, ruling that the charge alleged Bonds willfully used designer steroids dubbed "the cream" or "the clear" before the 2003.
Bonds admitted inadvertently taking designer steroids in 2003, but denied any use before then.
The jury will now consider four charges against Bonds. Two accuse him of lying about knowingly taking performance-enhancing drugs, a third charges him with lying about being injected by anyone but his doctors and the last is a catchall obstruction charge.
Bonds has pleaded not guilty to charges of obstruction and lying to a grand jury.
Anderson was taken to jail after he told Illston he was refusing to testify against Bonds, whom he grew up with in San Mateo County.
The Associated Press contributed to this report.