Addressing a press conference in Cairo in course of a whistle-stop tour through several Arab countries, Schroeder insisted the Israeli action was unacceptable.
"Violating the sovereignty of a third country complicates further the peace process, that's why what happened in Syria cannot be accepted," the German chancellor said.
Standing by his side, Mubarak lent his voice to criticising the Israelis.
"We condemn the violence and we condemn the aggression that happened today against a brother country under the pretext of the presence of Palestinian organisations," the Egyptian president said.
The Israelis reportedly struck at a civilian target near Damascus, claiming they were targeting an armed Palestinian group.
Calls for calm
Both Schroeder and Mubarak called for calm and said the best way to quell the escalating tensions could be political negotiations.
"I believe it is necessary to launch an immediate and effective action for a ceasefire and for both sides to start serious political negotiations," Mubarak said.
"Violating the sovereignty of a third country complicates further the peace process, that's why what happened in Syria cannot be accepted"
Schroeder and Mubarak met privately, before the German chancellor flew out to Saudi Arabia.
He is also scheduled to visit the United Arab Emirates before winding up his visit to the Gulf.
Travelling with a large business delegation, Schroeder is expected to focus on trade, reconstruction of Iraq and the Arab-Israeli conflict during his current tour.
Earlier during the day, Schroeder met Egyptian Prime Minister Atif Muhammad Ubaid and discussed joint projects in renewable energy, water resources, information technology, land and sea transport, telecommunications and sewage treatment plants.
The two also explored ways to increase German investments in Egypt.