Morgan Hill police arrested them at the Morgan Hill Inn at about 4:40 p.m.
The pair had stayed inside the room after blocking officers from entering by pushing furniture against the door at about 10 a.m., police Sgt. Troy Hoefling said.
Monterey Street, blocked all afternoon between Cosmo and Tennant avenues, was to be opened for traffic soon after the arrests, police said.
That stretch of Monterey Street, which turns into Monterey Road, is a business route through Morgan Hill about a mile west of U.S. Highway 101.
The standoff, involving a team of SWAT officers standing guard at the motel, was not a hostage situation as the man and woman chose to remain in their room at 16250 Monterey St., Hoefling said.
The man "made some statements about being armed" but police did not know during the standoff if he had any weapons, Hoefling said.
Police also talked to the woman "and gave her the opportunity to get out and she declined," Hoefling said.
They chose not to release the identities of the man and the woman during the standoff, Hoefling said.
The incident started this morning when a police officer on patrol by the motel noticed a silver Nissan Altima in the parking lot had different front and back license plates.
The officer investigated and learned that both plates had been reported stolen in San Jose, Hoefling said.
After finding the room associated with the Nissan, officers knocked on the door and heard a woman's voice say, "Hold on, let me get dressed," Hoefling said.
The officers then heard the shuffling of furniture to the door of the room, he said.
"They had no intention of opening the door," Hoefling said.
Police identified the man in the room as 29-year-old Martin Ceniceros Flores, from San Jose. He is on parole for an assault with a deadly weapon conviction, Hoefling said.
He also had a history of arrests for robbery, burglary, narcotics and domestic violence, Hoefling said.
Officers searched the Nissan and found property and mail they suspect had been stolen, he said.
All of the motel guests were evacuated and a car wash across the street was closed.