Ismail Haniyeh, head of the Hamas government that now controls the Palestinian security forces, said the order was aimed at easing tension.
Gun battles between police and militants began on Friday after the assassination of a leading member of the Popular Resistance Committees militant group.
Three people have died in the violence so far.
Israel denies any involvement in the car bombing that killed Abu Youssef al-Quqa and the PRC has accused Palestinian security forces of helping Israel to carry out the killing.
Haniyeh said: "What happened was dangerous and must not be repeated.
"The culture that dominated the Palestinian street in past years is a culture that needs time in order to turn into a culture that keeps law and order and does not resort to using arms under any condition."
The PRC said it had agreed to follow Haniyeh's call.
Elsewhere in Gaza on Saturday, Israeli artillery bombarded a unilaterally enforced no-go zone in the northern Gaza Strip after Palestinian militants launched three rockets overnight, an army spokeswoman said.
A Palestinian security source said that Israeli fighter-bombers had also attacked a Gaza City football stadium overnight, as well as a public park. The reason for the attacks was unknown.
Asked about the bombings, another Israeli military spokesman said: "We are deliberately attacking uninhabited sectors so as to spare the civilian population as much as possible.
"We want to give the Palestinians a clear warning that we will not accept the continued launching of Katyusha or Qassam rockets at our territory."