Lieutenant colonel Julian Leyzaola Perez was hit at around noon after his wife and daughter left his car to go into a shop near a border crossing into Texas, authorities said.
Authorities said he was in stable but serious condition after being hit in the neck, chest and back. He underwent surgery and his mobility could be affected, said Chihuahua state prosecutor Jorge Gonzalez Nicolas.
Two suspects aged 25 and 33 were detained in possession of guns and cocaine, and they face attempted murder charges, Gonzalez said.
The suspects said "they were ordered to kill someone, but they never knew who it was because they were only given instructions," he said.
Leyzaola Perez lives in Ciudad Juarez and works in a private security business. He was heading to neighboring El Paso, Texas, when he was shot.
He was the city's top cop from 2011 to 2013, AFP reported.
When he took over, Ciudad Juarez was in the grips of a drug cartel turf war, with murders peaking at 3,116 in 2010. The homicide rate has dramatically dropped since then.
Some credit Leyzaola Perez and a crime prevention program launched by the government, but security experts say the drop could mean that the Sinaloa cartel won the war against the Juarez gang.
The lawman had a controversial past from his days as police chief in the border city of Tijuana, where the police was accused of committing abuses.
On Thursday, the National Human Rights Commission urged the Chihuahua government to conclude an investigation into the April 2012 murder of four people, allegedly by Ciudad Juarez officers.