The crash over Ukraine killed 298 people, including 44 Malaysians.
Team spokesman Mohd Fahmi Omar said Tuesday that none of the 180 athletes and 72 officials in Glasgow were directly affected by the tragedy.
Their flag at the athletes' village was raised only to half-mast.
Unlike the Olympics, which does not allow political statements or any exterior messages on team uniforms, Commonwealth Games Federation president Prince Imran, who is Malaysian, said the federation had no problem with the armbands at the opening ceremony on Wednesday.
In February, Ukraine's Olympic Committee said the IOC rejected a request for its athletes at the Sochi Games to wear black armbands honoring those who died in violent protests in Kiev. Earlier in the Sochi Games, the IOC reprimanded Norwegian cross-country skiers for wearing black armbands in tribute to an athlete's brother, saying it would violate the Olympic charter.
''The Malaysian delegation has asked for formal approval from the organizing committee, and we expect there will be no issue, particularly for a situation such as this,'' Imran said Tuesday after a two-day federation congress.
Irman said he attended he attended the flag-raising ceremony and said it was ''very moving.''