The Nigerian man, 32, was arrested along with his wife, 31, at their bungalow in Lukut, near the capital's seaside resort area of Port Dickson, after a six-month surveillance operation, a report by The Star newspaper said.
The suspect is believed to have arrived in Malaysia less than a year ago, Director of Anti-Narcotics Investigations Department Commissioner Datuk Noor Rashid Ibrahim said.
Police also seized two cars -- a BMW and a Toyota -- from the Nigerian suspect who is believed to own several high-value properties in Malaysia.
"With his arrest, we hope to find out more about the syndicate's modus operandi and nab more suspects who worked for the syndicate in the days to come," Ibrahim said.
None of the arrested suspects was named by police.
The third suspect, a man believed to be the Nigerian's lieutenant, was arrested at an apartment in the wealthy Kuala Lumpur suburb of Taman Sri Hartamas.
Police said they found in his apartment packages totaling 62 pounds of the amphetamine known as syabu and 17 packages of heroin weighing 37 pounds in total.
Syabu, sometimes called ice, is a highly addictive crystal methamphetamine that is injected, snorted or smoked. It affects the central nervous system and users have wide mood swings, often suffering depression when the euphoria wears off.
The drugs were allegedly found in hidden compartments of bags, The Star report said.
Police also found a dozen other bags with hidden compartments that are believed to have been used for smuggling the drugs through customs at Kuala Lumpur International Airport.
"The women recruited by the syndicate fly into Malaysia ferrying the drugs in hidden compartments. They pass through KLIA before handing the bags to the syndicate contact person here," Ibrahim said.
The arrests of the three suspects come after other arrests last month in which police seized drugs with a street value of around $2.25 million.
Six people from Zambia, Iran and Nigeria, including women aged 25-38, were picked up at KLIA, the Kuala Lumpur satellite town of Damansara and in the city of Puchong.
Malaysia's police have been concerned about African involvement in drugs smuggling rings around the country, in particular their use of Malaysian women from remote areas to carry drugs through customs areas at international airports and through internal airports.
In July police said they were watching activities of suspected West African drugs syndicates in the states of Sabah and Sarawak on Borneo, a report in the New Straits Times said.
Continuous media coverage of drug mules and their plight in jails abroad has made it harder to recruit couriers in the larger cities on mainland Malaysia.
"This has forced these syndicates to look for drug mules in the interior areas of east Malaysia," said Ibrahim.
On June 30, two women from Sarawak were detained at a road checkpoint on the Malay-Thai border as they attempted to enter Malaysia. Authorities said they found nearly 25 pounds of syabu hidden in their baggage, the New Straits reported.