Judge Carlos A. Samour Jr. also ruled the jury will not be sequestered during the trial, which is scheduled to start in February and is expected to take four months.
Holmes is accused of killing 12 people and injuring 70 others at a movie theater in the Denver suburb of Aurora in July.
He has worn heavy shackles on his wrists and ankles during pretrial hearings. His lawyers wanted him to be unshackled during the trial, saying the restraints would make him look guilty to the jury.
Samour said Holmes has to be restrained because he is charged with violent crimes. He said jurors won't see the harness, and the anchoring cable will blend in with computer cables at the defense table.
The judge ruled earlier that Holmes can wear civilian clothing at his trial.
Holmes pleaded not guilty by reason of insanity to multiple charges of murder and attempted murder. Prosecutors are seeking the death penalty.
Defense lawyers wanted the jury sequestered and wanted the jurors barred from having phones, laptop computers or any other electronics devices during the trial.
The judge said sequestration for such a long time would be costly and impractical, and would create an undue burden on jurors. He implied it also could prompt some prospective jurors to try to avoid the case.
However, Samour said he would allow defense lawyers to renew the request later if they think they have grounds to do so.
Denying jurors access to smartphones, computers, television sets and radios - along with email and the Internet - would be drastic and unfair, the judge said.
But he did rule jurors will not be allowed to have the devices in court or during deliberations.
Samour said he might seat as many as 12 alternate jurors - an unusually large number - in the event any of the 12 regular jurors is dismissed for hearing outside information or other reasons.
"The court cannot keep the jurors in a bubble, completely sealed off from the outside world," the judge said.
Samour has said 5,000 potential jurors will get a summons and that he expects 3,200 to 3,500 to respond.
Holmes' lawyers had also asked the judge to scale back the heavy security that has been present during 11 months of pretrial hearings, saying it would be "extraordinary and unnecessary" during the trial and would prejudice the jury against Holmes.
They also objected to deputies standing so close to Holmes in the courtroom that they could hear his conversations with his attorneys.
Eight Arapahoe County sheriff's deputies usually stand guard in the courtroom during hearings. Others watch from the rooftops of the two courthouse buildings and in the parking lot.
Samour said four of the deputies in the courtroom will wear uniforms during the trial, and any others will wear street clothes. He also said they will keep a reasonable distance from the defense table.
The judge overruled the defense objection to having deputies on the rooftops and in the parking lot, saying they're necessary to protect Holmes and the public.
Samour said Sheriff Grayson Robinson had agreed to the hidden harness and tether for Holmes and the plainclothes deputies in the courtroom. Samour added he trusts Robinson's expertise and will heed his advice.