From October 1952 to July 1957, he served as the military attaché to the Indonesian embassy in Bonn, West Germany.

[2][4] In the early hours of 1 October 1965, several members of the 30 September Movement left Lubang Buaya on the eastern outskirts of Jakarta to seize key military figures and take them hostage.

Pandjaitan was among their targets, so they broke the fence near his house along Jalan Hasanuddin, Kebayoran Baru, South Jakarta.

Pandjaitan, then in full army dress, came from the second floor and allowed himself to be led away, stopping briefly to pray in his front yard.

After some minutes of irritatedly waiting for Pandjaitan to finish prayers, his captors lost their patience and shot him dead from behind.