Britain's new Social Democratic Party today chose Roy Jenkins, a senior figure in national politics, as its first leader, making him certain to be a candidate for prime minister in an alliance with the moderate Liberal Party at the next general election.

Jenkins, 61, who held a number of top positions in Labor governments and was president of the Commission of the European Community, defeated David Owen, 44, a former Labor foreign minister, in balloting among the party's membership. Jenkins received 55.7 percent of the vote and Owen 44.3 percent.

The balloting was another landmark in the creation of a third force in British politics with ambitions of offering a viable counterpoint to what its members believe is increasing polarization of the left and right in the two main parties.

The choice of Jenkins means that the party, which was founded in 1981 as a center-left alternative in Parliament to the Conservative and Labor parties, has staked its fortunes for now on a coalition with the well-established but perpetually third-place Liberals. The main policy difference between Jenkins and his opponent was that Owen favored looser ties with the Liberals.

The other differences between the two contenders were of style. Jenkins is cautious, more scholarly than bold, an aloof man who never seemed very comfortable with less cultivated colleagues, especially on the Labor left. Nonetheless, he served at various times as deputy Labor leader, home secretary and chancellor of the Exchequer.

Owen, nearly a generation younger, is brash and more openly opinionated. As Parliamentary spokesman for the new party, he overshadowed Jenkins in the tumultuous debates over the Falkland Islands crisis, in which both men basically supported the Thatcher government. Jenkins had been a clear favorite for the party leadership position until the Falklands came along, and last weekend a major poll showed Owen ahead.

Had Jenkins lost, political observers generally agreed, he would have been eliminated as a potential prime minister. Owen's strong showing, on the other hand, assures him a major role in developing party strategy as it struggles to secure a major place in British politics.

Six months ago--barely six months after the party was founded by, among others, Jenkins and Owen--the Social Democrats, in alliance with the Liberals, were polling well ahead of the Conservative and Labor parties in national samples. There was widespread speculation about a coming major realignment in British politics that would give the "Alliance," as it has come to be called, the balance of power in Parliament after the next election.

Today, that hope still remains among Social Democratic and Liberal activists but Alliance momentum has slowed significantly. The principal immediate cause is the Falklands, which gave the Tories a big political boost. In polls, Prime Minister Margaret Thatcher is now scoring at or near a clear majority over her combined opposition. But even before the Falklands, the Social Democrat-Liberal standing had dropped to virtually equal with Labor and the Tories despite victories in Parliamentary by-elections.

Jenkins appeared this evening at the musty party headquarters near the House of Commons to have his picture taken in various smiling poses. But he declined to make a formal statement or take detailed questions, preferring instead to call a Saturday press conference that assures him two days of major coverage here and extensive stories in mass-circulation British Sunday newspapers.

He did say, however, that he believes that public opinion will now turn again from the Falklands victory to the country's severe economic problems, particularly the highest unemployment in 50 years. "Despite all the optimistic predictions" of the Thatcher government, he said, "the economy is still in trouble." His selection, he said, will give the Social Democrat-Liberal Alliance the "great" push it needs to again excite public interest on a wide scale.

Out of a total of 62,372 paid-up party activists, 75.6 percent or 47,187 voted, which officials of the party hailed as a heavy turnout for a mail-in ballot. Jenkins received 26,256 votes and Owen 20,864.

In his brief comments, Jenkins also stressed the importance of a "united" Alliance with the Liberals in the election expected in the fall of 1983 at the earliest. His counterpart as leader of the Liberals, David Steel, welcomed Jenkins' victory in a statement but also praised Owen as "crucial to any Alliance government."

The minimum Jenkins-Steel goal appears to be to win about 100 seats in the next Parliament, thereby denying both the major parties a majority. Then the Alliance would seek to form a coalition with moderate Conservatives, ousting Thatcher and instituting a change in Britain's voting to proportional representation--based on results nationwide instead of the majority in each constituency winning the seat. This would virtually assure an important place for a third major British party in the coming years.