Dubbed the Suez Canal Axis, the new 72-kilometre project is aimed at speeding up traffic along the existing waterway by reducing the waiting period of vessels, as well as boosting revenues for Egypt.
It will run part of the way along the existing canal that connects the Red Sea to the Mediterranean.
"The first trial run for ships passing through the new Suez Canal started today," state news agency MENA reported.
The fleet sailing from south to north had vessels flying flags of Singapore, Luxembourg and Bahrain. Those sailing from north to south had flags from Liberia, Singapore and Hong Kong.
The new waterway involves 37 kilometres of dry digging and 35 kilometres of expansion and deepening of the Suez Canal, in a bid to help speed up the movement of vessels.
President Abdel Fattah al-Sisi launched the project in August and set an ambitious target of digging the expanded canal within a year.
The canal is part of an ambitious plan to develop the surrounding area into an industrial and commercial hub that would include the construction of ports and provide shipping services.
The new route is considered a "national project" that aims to kick-start an economy battered by years of political turmoil since the ouster of president Hosni Mubarak in 2011
Authorities raised $9 billion (7.9 billion euros) to build the new canal by selling shares in the project to domestic investors, with private Egyptian companies tasked with its construction.
Built 146 years ago, the Suez Canal is one of the world's most heavily used shipping lanes and has been a key source of international trade.