The Rev. Adrian P. Rogers, fundamentalist-backed pastor of a 16,000-member Memphis church for 14 years, was elected president of the Southern Baptist Convention today, capturing 54 percent of the votes of the nearly 40,000 delegates at the annual meeting.

Rogers, 54, defeated the Rev. W. Winfred Moore, 66, a pastor for 27 years in Amarillo, Tex., and unsuccessful flag-bearer for the church's moderates in the last two elections.

The election of Rogers, active in various causes favored by the religious right and SBC president in 1979-80, is expected to accelerate the turn to the right that has increasingly divided Southern Baptists in recent years.

His victory caps a determined seven-year drive by fundamentalists for control of the denomination. Fundamentalists hold that the Bible is literally true.

Rogers told reporters today that he does not "believe we are divided 55 to 45" percent, as the presidential vote appeared to indicate. "I think it's more like 90 to 10."

Rogers said his appointments as president will reflect a 90-to-10 ratio. The SBC president appoints members of committees that, in turn, determine membership of the denomination's 20 national policy-making boards and institutions.

Asked if he would support women clergy, he said, "I do not believe the Bible teaches ordination of women."

The Rev. Charles Stanley of Atlanta, retiring president and a fundamentalist, defied Baptist tradition in his presidential address, delivering a thinly veiled but rousing speech for Rogers.

Stanley warned the convention that Baptists "face the possibility of a generation of barrenness if we don't have the courage [to] keep on moving in the direction we are going in . . . . "

The church, Stanley said, "must follow a policy of positive reporting and avoid changing the policy of leadership at a crucial time in the Southern Baptist Convention."

Moore, who as first vice president chaired the session, sat impassively on the platform during Stanley's address.

In a subsequent business session, Kent Anglin of Hartwell, Ga., proposed that at future conventions the election be held nearer the opening of business, in order to discourage "using the presidential address time . . . for advocating personal and philosophical positions."

At the start of the business session today, the Rev. Donald White of Uppercove, Md., proposed giving each presidential candidate 10 minutes to address the convention.

"Let the people make up their minds on the basis of that," White said, "rather than through the rhetoric we have been hearing."

Stanley ruled the proposal "out of order, because you can't compel another man to speak."

Several resolutions and parliamentary points of order offered today reflected the hostility and suspicion that has beset the church in recent years.

Even a letter of greeting from President Reagan caused sparks. Reagan expressed satisfaction that "the liberalism [in the nation] that seemed triumphant has been turned on the defensive."

Warning against complacency, he asked Baptist support for efforts to overturn abortion on demand and laws that "deprived children the right to pray together in the schools you pay for. They may no longer declare their gratitude and dependence on God or ask His help."

Most moderates disagree sharply with these stands. One "messenger," as the convention delegates are known, challenged the decision to read Reagan's letter during the business session.

"I find it ill-timed and hostile," he said.

Another delegate complained that he "saw with my own eyes a woman voting two ballots," and demanded that the vote be retaken.

But a parliamentarian ruled that the balloting need not be repeated "unless one of the candidates wins by only one vote."