Protests over the weekend paralyzed Deir el Balah in central Gaza, home of the brothers.
Militant groups had vowed retaliation last Sunday after Israeli forces killed 14 people, most of them gunmen, in a raid into central Gaza.
Fierce fighting in the Maghazi refugee camp in central Gaza left at least seven Palestinians dead.
The army confirmed only that its troops had entered central Gaza.
Before dawn Wednesday, the military hit three buildings in northern and central Gaza that it said were used by various armed Palestinian factions.
An airstrike in central Gaza targeting a car killed a Palestinian militant, his 5 year-old son, and his brother.
Most border crossings were closed and Israeli forces eventually moved into central Gaza, cutting the roughly 28-mile-long strip in two.
Hours later, Israeli forces swept into two camps in central Gaza, killing at least four Palestinians.
In central Gaza, three rockets were fired at another wanted militant in an open field but missed him.
Hamas security men laid siege on a house where the suspects were staying, in the Nusseirat refugee camp, in central Gaza.