Charles Njonjo, who was for many years a key politician in Kenya's government, was stripped of the last of his power yesterday when he was suspended, at least temporarily, from the Kenya African National Union, the country's sole political party.

The decision by a special meeting of the party's governing council will keep Njonjo out of the party until a judicial inquiry releases its findings on charges of "serious irregularities" allegedly committed by the former Cabinet minister. If the inquiry's ruling is unfavorable, observers here said, the party is expected to expel Njonjo permanently.

The suspension is expected to keep Njonjo from seeking a seat in the National Assembly when elections are held in September. Only party members are eligible to be candidates.

Njonjo's suspension follows a rapid fall from power this spring that appears to have been orchestrated carefully by officials here. In early May, President Daniel arap Moi told a fund-raising rally that "a traitor" was being groomed by "foreign powers" to take over the presidency. During the weeks that followed a whirlpool of accusations and innuendo created by other members of parliament and party officials pointed to Njonjo as the suspect. By the end of June he had been effectively stripped of any political credibility.

Although he twice publicly denied the allegation, Njonjo was named in Parliament as "the traitor" by Tourism Minister Elijah Mwangale last month. On June 29, Moi relieved him of his post as minister for home and constitutional affairs and appointed the inquiry.

The party's move eliminates the prospect of a powerful rival to Moi. In the past, Njonjo was considered to be second in power only to the president because of his close ties to Kenya's two leaders. His influence began during the latter years of the administration of Jomo Kenyatta, who led Kenya to independence in 1963, and continued for some time after Kenyatta's death in 1978, when Moi became president.

Njonjo, who is known for his Saville Row pinstripes and British-oriented habits, also provided a line of communication for many western diplomats and Kenya's commercially influential expatriate community.

Although the alleged foreign involvement in the Njonjo issue never has been traced publicly, there have been isolated accusations by politicians that Njonjo has aligned himself with Israel and South Africa, two countries that are unpopular in black Africa, and has maintained economic interests in South Africa.

Since early June visitors flying to Kenya from South Africa have been refused entry regardless of their nationality. Kenyans say the ban resulted from a fear of South African support of some candidates in the election.

Njonjo, who was educated in Britain, also is known to have staunchly supported the United States and Britain. No public reference has been made to this, but privately several legislators have voiced their grievance over his supposed backing by the United States. The Reagan administration strongly supports the Kenyan government because of its strategic importance, although both countries recently have been at pains to give the friendship a low profile.

Kenya is perceived by the administration to be an essential link in a line of U.S. allies along the east coast of Africa that includes Egypt, the Sudan and Somalia. Under a 1982 agreement, significant improvements have been made to the port of Mombasa to enable it to be used as a supply point for U.S. Navy warships in the Indian Ocean.

Although Kenya is a relatively unimportant African export market for the United States, it is one of the United States' larger aid and arms beneficiaries on the continent. The U.S. aid package to Kenya for 1984 is expected to be between $80 and $100 million. The Reagan administration also has exhibited help in other ways.

Analysts say the Reagan administration has pressured the World Bank and the International Monetary Fund to continue to give vital balance of payments support despite doubts over the execution of conditions attached to the loans. The United States also stepped in with an additional balance of payments loan of about $28 million to help close a critical gap in the national budget just before the end of Kenya's financial year this June.

Meanwhile, observers here said they expect Njonjo's downfall to be the beginning of a careful whittling away of unwanted political characters by Moi. Electorate apathy is evident through the poor voter registration--just more than 50 percent even though the registration deadline was extended by a week. But for Moi, whose government was shaken when there was an abortive coup attempt by junior Air Force officers last August, the election outcome is vital to his future security.