The Israel Defense Forces says a unit from its 828th Bislamach Brigade was patrolling Tal al-Sultan, an area of Rafah, on Wednesday.
Three militants were identified and engaged by the Israeli troops – and all were eliminated.
At that stage nothing seemed particularly remarkable about the firefight and the soldiers did not return to the scene until Thursday morning.
It was then, as the dead were inspected, that one of the bodies was found to bear a striking resemblance to the leader of Hamas.
The corpse however remained in situ due to suspected booby traps and instead, part of a finger was removed and sent to Israel for testing.
His body was finally extracted and brought to Israel later that day as the area was made safe.
Daniel Hagari, the IDF’s spokesman, said that his forces “didn’t know he was there but we continued to operate”.
He said that his troops had identified the three men running from house to house, and engaged them before they split up.
The man since identified as Sinwar “ran alone into one of the buildings” and was killed after being located with a drone.
None of the hostages Sinwar was believed to be using as a human shield were present and his small retinue suggests either he was trying to move unnoticed, or had lost many of those protecting him.
Yoav Gallant, Israel’s defence minister, said:: “Sinwar died while beaten, persecuted and on the run – he didn’t die as a commander, but as someone who only cared for himself. This is a clear message to all of our enemies.”