Shaheen Murad, 37, Hassan Raza, 21, are alleged to have killed David James Ginter, 62, on May 4.
No plea was recorded from the two unemployed accused, who face the death penalty.
Two other accused are still at large.
On June 13, a Pakistani security guard, Shahbaz, 25, was charged with the same offence.
Ginter was reportedly found with his hands and feet bound and a mobile phone charger cable wrapped around his neck in his double-storey house on the outskirts of Kuala Lumpur.
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The next court date is set for July 18.
The motive behind the murdrer was still unclear though robbery had been earlier cited by the police.
Ginter had been a senior pastor at the Bridge International Church in Kuala Lumpur for three years.