A statement said that the frigate Karlsruhe had responded to a distress call from the Wabi al Arab which was under attack off the coast of Yemen at around 0745 GMT.
The pirates called off their attack after helicopters were dispatched from the Karlsruhe and a sister frigate, the Mecklenburg-Vorpommern, but were still in the area, the communique added. The Navy said that the Mecklenburg-Vorpommern was currently heading to the aid of another ship, called the Hatef, whose nationality was not specified, which had also called for help.
The International Maritime Board (IMB) piracy reporting centre in Kuala Lumpur praised the quick reaction of the Germans in an earlier statement.
Noel Choong, head of the centre, said the Egyptian vessel was sailing from the Suez Canal to Asia with 31 crew on board when attackers opened fire on it with automatic weapons.
"A passing ship relayed the pirate attack incident to the IMB. We informed the coalition forces and the German warship was deployed to the scene. Their fast response prevented the hijack," he said.
Choong said the seafarer who was shot was picked up by another helicopter for medical treatment of a leg injury on board the German warship.
"Pirates are still active despite the presence of coalition forces. They are finding loopholes to launch their hijack attempts," he said.
Patrols off the Horn of Africa that were, until recently, carried out by NATO ships are now being done by a European Union task force.
The frigate Karlsruhe set sail only on Tuesday from Djibouti to take part in the EU-led anti-piracy mission off the Horn of Africa. The waters in the region have been plagued by increasingly daring attacks by pirates, mostly from Somalia.
Japan said Thursday it was considering dispatching a destroyer to waters off Somalia to guard against the pirates, who are inflicting a costly toll on the shipping industry.
Pirates have carried out 110 attacks in the key shipping lanes of the Gulf of Aden, located between the south of Yemen and the north of Somalia, and the Indian Ocean east of Somalia since the start of this year.
Last month, they captured the world's attention when they hijacked the Saudi-owned super-tanker Sirius Star, carrying two million barrels of crude oil, and demanded a $25-million ransom for the ship and its crew.