There were conflicting reports concerning which of the terrorists was killed.
Israeli security officials said Ahmed Ismail, 22, was killed and his partner Eid Okel Hjazi, 19, of Rafah was injured in the strike. Israel Radio said Hjazi was taken to a local hospital in Gaza.
Palestinian reports in Gaza said Hjazi was killed and Ismail injured.
Shortly after the incident, Palestinians in Gaza fired a Qassam rocket at Sderot, no injuries or damage was reported, Israel's Channel One television said. A number of mortar shells were later fired at southern Israel, Channel Two reported.
The army said Ismail and Hjazi were plotting a terrorist attack along the Israel-Egypt border. Military spokesman Yoav Mordechai told the Hebrew language newspaper Maariv the attack was already in the advanced planning stages and was to be carried out on the Eilat-Egypt border. The airstrike thwarted the terrorists' plans, he said.
Prime Minister Binyamin Netanyahu issued a statement praising the army and security agency saying "all those who intend to harm us should know our long arm will reach them."
The army said the two were part of a group who attacked Israeli workers building the border fence along the border with Egypt in June, an incident in which one Israeli was killed.