Roberto Orduña Cruz, the city's public safety secretary, said he didn't want to risk more lives. An officer and a jail guard were shot to death earlier Friday, two days after handwritten signs were posted saying a policeman would be killed every 48 hours unless Orduña resigned.
"Respect for the life that these brave officers risk every day on the streets for Juarez residents obliges me to offer my permanent resignation," Orduña said.
The departure is the latest blow to law and order in the border city, which has become the deadliest corner in Mexico. Killings have soared in the last year because of a turf war between drug-trafficking groups and because of the Mexican government's crackdown on smugglers.
More than 1,350 people died in Juarez last year in violence that included numerous beheadings and the killings of more than 60 police officers.
Drug gangs have shown no sign of backing down in the face of a government offensive that has sent 3,000 soldiers into the streets of Juarez. Unofficial tallies by the news media put the death toll so far this year at more than 300 in Chihuahua state, where Juarez is located.
On Wednesday, half a dozen of the handwritten signs were posted in Juarez.
A day earlier, the city's second-ranking police officer, operations chief Sacramento Perez, was fatally shot, along with three other agents, near the U.S. Consulate in Juarez.
Mayor Jose Reyes Ferriz had said he would not back down in the face of threats.
But Friday afternoon, Reyes and Orduña appeared at a news conference to announce the chief's resignation.
Orduña, a retired army major, took the job in May after his predecessor, Guillermo Prieto Quintana, quit and fled to Texas after his second in command was gunned down.
Orduña seldom ventured from the police station and even slept there -- one sign of how little control authorities have over Juarez's streets.
He presided over a department rife with corruption. Reyes dumped more than 300 suspect officers in October. Statistics indicated that there were fewer bank robberies after they were fired.
Reyes said Friday that Orduña's resignation was not a surrender to organized crime. "It's understandable that the major's first concern was his officers," he said.
A replacement has not been named.
Cecilia Sanchez of The Times' Mexico City Bureau contributed to this report.