Senate Republican leaders yesterday spurned a last-minute appeal from President Reagan to accept the House version of his spending cut plan and insisted on going to conference on the nearly $40 billion in program cutbacks.

The decision to buck the White House amounted to at least a tentative reassertion of congressional prerogative over economic policy, which has so far been dominated by Reagan and his budget director, David A. Stockman. It also constituted a go-easy signal to Stockman, whose go-for-broke style of lobbying has frayed some sensitive nerves on Capitol Hill, especially in his latest effort to short-circuit the House-Senate conference on the spending "reconciliation" bill.

While agreeing with Reagan and Stockman that there are risks in a conference, Senate Majority Leader Howard H. Baker Jr. (R-Tenn.) and Budget Committee Chairman Pete V. Domenici (R-N.M.) said they nonetheless believed it would produce a better bill.

Moreover, negotiations with Democrats to produce a smooth, minimum-risk conference had reached the point that "I do now predict we will pass a reconciliation bill within the next week or so," Baker told reporters after activating the machinery to begin a conference early next week.

Reagan called Baker yesterday morning to throw his weight behind Stockman in urging the Senate Republican leadership to consider accepting the House-passed version of the spending cuts instead of risking a conference stalemate or rejection of a conference compromise on the floor in the Democratic House. Stockman had lobbied hard over the last few days to get the Senate simply to accept the House bill.

Baker submitted the issue to committee chairman and other GOP leaders, who voted 19-to-2 to insist on a conference. Only Appropriations Committee Chairman Mark O. Hatfield (R-Ore.) and Sen. Roger W. Jepsen (R-Iowa), vice chairman of the Joint Economic Committee, dissented, according to Senate Republican sources. Baker told Reagan of the decision during a meeting on another issue at the White House and reported afterward at a news conference that the president "heartily endorsed the decision once it was made."

It was the second time in recent weeks that Senate Republicans rebuffed a Reagan initiative on economic strategy. The first came when the Senate unanimously endorsed a GOP resolution rejecting Reagan's main proposals for Social Security cutbacks.

Both Baker and Domenici went out of their way to downplay the dispute as "an honest disagreement on the last step of the [budget] process," as Baker put it, although Domenici made a point of publicizing his disagreement with Stockman on the conference issue.

Sources said it was Domenici, principal architect of the Senate reconciliation bill, who led the fight to resist Stockman, resulting in what was described as a strongly worded lecture from Domenici to Stockman yesterday morning about senatorial responsibilities.

To the extent that there were winners or losers in the episode, Domenici was a winner and Stockman a loser -- so long as the conference does not bog down.

"I know it's a great risk," Domenici told reporters. "I don't want to lose this package any more than anyone else. But I belive we will get reconciliation . . ."

Asked about reports that Senate Republicans might reserve the option to resurrect and approve the House bill if the conference falters, Baker said the Senate was "not without remedies." But he did not appear to stress any fallback strategies.

In congressional shorthand, reconciliation means program cuts designed to meet budget targets: in this case nearly $40 billion worth of cutbacks in domestic programs to achieve a scaled-back spending target of $695.5 billion for fiscal 1982. Even the Democrat-controlled House adopted most of Reagan's proposed cuts when conservative Democrats voted for a Reagan-backed substitute to cuts that had been proposed by House Committees.

While the House and Senate versions were "almost identical" in about 75 percent of their provisions, according to Baker, he and Domenici said the differences were important enough to merit a conference.

Moreover, Domenici said even some House Republicans were sufficiently disturbed by some aspects of their hastily prepared, error-pocked bill to tell senators they wanted a conference to clean up the legislation.

According to Domenici, the critical substantive differences between the two versions include Medicaid financing, food stamps and nutrition, health block grants, Conrail funding and non-budgetary items like radio and television deregulation.In all, there were "important areas of disagreement that senators felt very strongly about," both Republicans and Democrats.

While there is basic agreement on cutbacks in entitlement programs, which the White House stressed in pushing for the GOP alternative in the House last month, there are 30 to 40 other issues to be resolved, Domenici said.

Baker discounted speculation that a conference might eliminate "sweeteners" that House Republicans inserted to patch together their 217-to-211 victory on the reconciliation bill last month. He said he thought the conference would probably produce a compromise that would pick up more votes than it would lose.