Superior Court Judge Michael Sweet did not allow reporters to take video, audio or send out tweets during the hearing.
DeAngelo's public defender, Diane Howard, filed the motion to block efforts by the district attorney to take DNA, fingerprints and photos of DeAngelo's body.
In court, 72-year-old Joseph James DeAngelo appeared in a wheelchair again, was clean shaven, handcuffed and seemed to look confused.
He did not make eye contact with anyone in the room but his attorney.
During the hearing, Judge Sweet rejected the motion issued by DeAngelo's defense.
Investigators will be allowed to collect DeAngelo's DNA and take photographs of his body; Sweet called the items "non-testimonial."
Sacramento County District Attorney Anne Marie Schubert got the warrant last week.
DeAngelo was arrested last week and identified as the suspect in at least a dozen murders and more than 50 rapes between 1976 and 1986.
Prosecutors said they used DNA and a genealogical website to identify DeAngelo, decades after the case had gone cold.
Prosecutors initially planned to take more DNA and photographs Wednesday, prompting Howard's motion to halt the action.
Howard argued in a motion that the search warrant should be stopped because it was approved before DeAngelo was arrested and arraigned last week.
Prosecutors argued that the search warrant was still relevant and said collecting the evidence won't be "testimonial in nature."
The Associated Press and other news organizations have filed a motion to unseal the full search and arrest warrants for DeAngelo, which could provide additional details about the DNA techniques prosecutors used to identify him.
DeAngelo is due back in court on May 14. He has yet to plea to the murder charges he is facing.