The German military said on Tuesday the brigadier general, named by the German media as Michael Bartscher, was wounded in the attack, but was not in a life-threatening condition. His family has been informed.
The general, one of four German generals in the country, was injured when a man in an Afghan soldier's uniform opened fire at a British-run military academy in Qargha, west of Kabul, at 10am German time.
A two-star US general, named as Major General Harold Greene, was killed in the attack and at least 15 ISAF soldiers were injured. Greene was one of the leaders of the US military's training programme in the country.
The Afghan Defence Ministry said a "terrorist in the uniform of the national [Afghan] army," had opened fire on both Afghan and foreign troops. The generals had been holding a so-called "Key Leader Engagement" meeting at the academy.
"We suspect the attacker was an Afghan soldier," Pentagon spokesman John Kirby said.
Germany's Foreign Office condemned the attack as "despicable", adding that ISAF soldiers were engaged in the country at "great personal risk" to give Afghans a better future.
The Taliban praised the attacker as a "hero." He was killed in the incident.
Germany currently has around 2,000 troops in the country, mainly based in the north.
The attack comes three days after German troops officially changed their mission from a combat to training and assisting Afghan security forces.