Male Fu Wa and female Feng Yi, both 8 years old, are on a 10-year loan from China to commemorate the 40th anniversary of diplomatic ties between the two countries.
Upon their arrival in a special plane, they were taken to a specially built complex at Malaysia's national zoo outside Kuala Lumpur, where they'll be quarantined for a month before receiving visitors.
The pandas' scheduled arrival last month was postponed out of respect for relatives of passengers aboard Malaysia Airlines Flight 370. The plane vanished while flying from Kuala Lumpur to Beijing on March 8 with 239 people on board, mostly Chinese, and the search for the aircraft is ongoing.
"May the arrival of these two precious icons of China contribute to building an everlasting friendship and sustainable cooperation" between the two countries, said Malaysia's environment minister, Palanivel Govindasamy.
Palanivel said 60 million ringgit ($18.6 million) had been allocated for the pandas, including a 25 million ringgit ($7.7 million) air-conditioned conservation complex at the zoo.
He said he hoped the two pandas would be able to mate and breed in their new home.
China has long used "panda diplomacy" to make friends and influence people in other countries.
Some of the relatives of Flight 370's passengers and other Chinese have expressed anger over Malaysia's perceived mishandling of the plane's disappearance. The kidnapping of a Chinese woman from a Malaysian island resort in early April was also a blow to the country's image in China.
At least 30,000 Chinese tourists have canceled vacation plans to Malaysia since the plane disappeared. About 1.6 million Chinese tourists visited Malaysia last year.
Malaysia's government says satellite data showed the jet crashed into the southern Indian Ocean, but no wreckage has been found despite an exhaustive multi-nation search. Authorities believe the plane was flown deliberately off course, but are still investigating the cause of the disappearance.
The search has moved into a new phase, with an underwater hunt led by Australia. A Chinese navy survey ship will start mapping the seabed off the west Australian coast this week.
