In an interview with the state-run Al-Thawra newspaper printed in full Thursday, Assad praised Egypt's popular protests against their leader, adding that Morsi’s overthrow by the military means the end of "political Islam”.
Assad said the great nation of Egypt has discovered the "lies" of the Muslim Brotherhood.
"What is happening in Egypt is the fall of so-called political Islam," Assad said. "This is the fate of anyone in the world who tries to use religion for political or factional interests."
"You can't fool all the people all the time, let alone the Egyptian people who have a civilization that is thousands of years old, and who espouse clear, Arab nationalist thought," he added.
"After a whole year, reality has become clear to the Egyptian people. The Muslim Brotherhood's performance has helped them see the lies the (movement) used at the start of the popular revolution in Egypt."
Earlier Wednesday, Syrian Information Minister Omran al-Zoubi urged Egyptian President Mohammed Morsi to step down in line with his people's wishes.
Al-Zoubi told reporters in Damascus that Morsi's Muslim Brotherhood is a "US tool."
Last month Morsi enraged Syrian officials by announcing he was severing ties with Damascus and closing its embassy in the Syrian capital.
Assad's father, the late President Hafez Assad, cracked down on a Muslim Brotherhood-led rebellion in the northern city of Hama in 1982.
Mursi has expressed support for foreign intervention against Assad and attended a rally two weeks ago calling for war in Syria.