A Senate committee turned back the first major challenge to the Clean Air Act yesterday, refusing on a decisive 12-to-3 vote to bring economic factors into the setting of secondary air pollution limits that protect the environment and public welfare.

In what could be a significant indicator of the degree to which the act will be changed, Senate Majority Leader Howard H. Baker Jr. (R-Tenn.) and Sen. Pete V. Domenici (R-N.M.) both voted with the winners against the proposal. Domenici has been a leading critic of the 1970 act.

The Reagan administration had taken no formal position on the shift, but most of its draft rewrite proposals had favored adding economic factors to the list of criteria to be considered in setting a target ceiling on pollution levels.

"This could mean they Republicans realize they aren't going to get any major changes," said one environmental lobbyist.

Tossing out the window dozens of laborious drafts of a total Clean Air Act overhaul from the administration, lobbyists and its own staff, the Environment and Public Works Committee opened its first full rewriting session by considering only amendments to the law itself.

Sen. Robert T. Stafford (R-Vt.), the committee chairman, has said repeatedly that only moderate changes in the law will get past him to the Senate floor, but he failed in his effort to produce a proposed rewrite that all sides could live with. The committee now plans to consider the law section-by-section "until Christmas if necessary," Stafford said, voting on individual amendments as they arise.

Sen. Steve Symms (R-Idaho), who appears to be acting at least in part as a voice for the administration's point of view, offered the economic amendment to the section of the law governing so-called secondary standards. Tighter than the primary standards, which are set at levels that protect human health, the secondary standards are to protect crops, visibility and plant and animal life from damage by air pollution.

Symms argued that the law now "might require a standard that would halt industrial growth in the Northeast" in order to protect "a few palm trees in Florida," since standards now must be set to guard the public welfare against "any known or anticipated adverse effects." His amendment would have required the Environmental Protection Agency to consider "social and economic consequences" in setting secondary standards.

It would also have eliminated the word "any" in order, Symms said, "to inject a little realism" into the bill. Sen. George J. Mitchell (D-Maine) said the change would be "a fundamental deviation" from tradition and precedent and would "undermine the premises" of the law and substantially weaken it. The committee vote agreed with him.

Symms also withdrew another amendment that would have added an economist to EPA's science advisory board when committee sentiment appeared clearly against it. That amendment would have expanded the seven-member board "so that economic benefits can be considered" when EPA evaluates scientific data to decide whether an air pollutant needs controlling, Symms said.

Sen. John H. Chafee (R-R.I.) opposed the idea on grounds that it might be a precedent for adding energy, health, welfare and social experts to the board. Sen. Slade Gorton (R-Wash.) opposed the measure, too. "What I think it does is provide another source for lawsuits," he said.