The fighting took place after Israel on Tuesday killed Baha Abu al-Ata, one of the PIJ's most senior commandersm in the Gaza Strip in an air strike.
While a PIJ spokesman told the BBC that the ceasefire came into effect at 5.30 a.m. on Thursday, Israel was yet to confirm the development.
But UN Special Coordinator for the Middle East Peace Process Nickolay Mladenov announced on Twitter: "Egypt and the UN worked hard to prevent the most dangerous escalation in and around Gaza from leading to war. The coming hours and days will be critical.
"All must show maximum restraint and do their part to prevent bloodshed. The Middle East does not need more wars."
The launch of rockets from Gaza did not stop early Thursday despite reports that the truce would come into effect.
Anti-aircraft sirens continued to sound until 7 a.m., when the last alert was activated in the neighbourhoods bordering the Gaza Strip, and relative calm returned.
The Gaza health ministry said early Thursday that two more Palestin had died in southern Gaza and six in the central part, taking the total number of casualties since Tuesday to 34.
According to security forces in Gaza, the shelling on Thursday morning also hit sites of other small Palestinian militias.
( With inputs from IANS )