The Israel Defense Forces said the strikes, which were carried out north of Jabalya and east of Gaza City, targeted militants who were engaged in firing Qassam rockets at Israel.
One of the militants was identified as Ayman Cahouji, a member of Hamas.
No injuries were reported in the rocket attack on Sderot, but the building, which was empty at the time, suffered severe damage.
Also Tuesday, official censorship was lifted on the fact that a Katyusha rocket fired in recent days from the Gaza Strip struck near the home of Public Security Minister Avi Dichter in the southern coastal city of Ashkelon.
Late Monday, the IAF fired a missile at a group of Palestinian militants firing rockets from the northern Gaza town of Beit Hanun, killing one man, Palestinian officials said.
A second strike in the same area caused no casualties, they said.
The IDF confirmed both strikes, saying the first hit a rocket squad and the second struck a donkey cart loaded with rockets.
Earlier Monday, an Egyptian helicopter on Monday accidentally violated the airspace of the Gaza Strip, and was escorted by IAF aircraft back into Egypt's airspace.
Also on Monday, the IDF pulled its ground troops out of the Gaza Strip, and Hamas seized the pullout to declare "victory" in the intensive fighting that has killed more than 100 people in recent days.
The pullback followed days of sequential fighting that drew an appeal from Washington to end violence and rescue peace talks with the Palestinians.
The withdrawal came after the IDF senior command on Sunday recommended keeping up intensive military pressure on Hamas.
Medics and Hamas have said about half of those killed in recent days have been civilians, including women and children, but IDF Chief of Staff Gabi Ashkenazi said that of the 100 fatalities, 90 were armed militants.