The eight-year-old pandas will be housed in a 1.6 hectare air-conditioned complex at the national zoo. China agreed to loan them to Malaysia to mark 40 years of diplomatic ties this year.
But Beijing postponed their delivery because of disagreements over the Malaysian authorities' handling of the disappearance of flight MH370. Most of the passengers on board the Malaysia Airlines plane were Chinese, and their relatives have accused the authorities of mishandling the search for the plane.
But the pandas, called Fuwa and Fengyi which means "lucky child" and "phoenix" in Mandarin, are being seen as a peace offering, reported BBC.
China has often used "panda diplomacy" to strengthen ties, and has sent pandas to the United States, Singapore and Japan in the past.
Local media has expressed excitement, with by-the-minute coverage of their arrival and exuberant headlines such as "Panda-monium erupts, they are here!"
Local authorities said the pandas will be quarantined for a month before the public can view them.