Deborah Madden entered her plea before U.S. District Judge Susan Illston. The crime is punishable by up to a year in jail.
Madden declined to comment about her plea, but her defense attorney, Paul DeMeester, considered it a victory in the more than three-year-old saga.
"A misdemeanor disposition is always good given that the federal government brought all of its immense powers to bear on poor Debbie Madden," DeMeester said. "It's a win for us."
Madden, 63, of San Mateo was at the center of a scandal that resulted in hundreds of drug cases being dropped after she was accused of taking small portions of cocaine from crime lab evidence lockers in late 2009.
She was on a leave of absence when an audit revealed the missing cocaine. She retired a short time later after 29 years on the job.
The fiasco led to a temporary closing of the lab before it was reaccredited in 2010.
State prosecutors declined to file charges against Madden, citing insufficient evidence. A federal grand jury then indicted her on a felony charge of obtaining cocaine by fraud, deception or subterfuge.
DeMeester said his client was made a scapegoat for the overall shortcomings of the crime lab. He said that he will seek probation for his client, who is now studying for a degree in substance abuse counseling.
Madden's plea came after two mistrials in federal court, as jurors could not reach unanimous verdicts.
After the second mistrial in January, federal prosecutors offered to drop the felony charge in exchange for a guilty plea to misdemeanor theft, the same offer DeMeester initially made for his client.
"Two juries later, we are exactly where we wanted to be from the very start," he said Friday.
Madden is scheduled to be sentenced in July.