Air raid sirens sounded across northern and southern Israel around 5:00am local time, shortly before the impacts.
The Israeli army said Iran launched between 10 and 15 ballistic missiles in six salvos, according to statements carried by local media.
The attack lasted more than an hour, Al Jazeera reported.
Emergency services responded to multiple strike sites, including the heavily damaged apartment block in Beersheba.
Firefighters and Home Front Command soldiers later recovered the body of a fifth victim from the rubble, according to the Fire and Rescue Service.
Two of the wounded were reported in moderate condition.
The strikes occurred four hours after US President Donald Trump said at 1:00am Cairo Local Time (CLT) that Iran and Israel had agreed to a truce.
He declared the ceasefire officially in effect at 8:08am CLT.
Israel confirmed its acceptance around 9:10am CLT.
Iran, however, denied that any agreement had been reached. Foreign Minister Abbas Araghchi said Tehran would halt its operations only if Israel ended its “illegal aggression.”
Short link: