The Senate, led by rebellious Republicans from campaign battleground states in the Midwest and Pacific Northwest, defied the Reagan administration yesterday in moving to protect low-cost power in the two regions.

Brushing aside veto threats from the White House, it followed the lead of Sen. James Abdnor (R-S.D.), one of the GOP's most endangered incumbents in this fall's elections, and approved a loan-refinancing plan for rural electrification systems, which critics said would end up costing the government $2.4 billion at current loan values.

Then, under prodding from Pacific Northwest senators, including Slade Gorton (R-Wash.), who also faces a less severe but potentially difficult Democratic challenge this fall, it voted to block the administration from spending any more money on planning the sale of government power-marketing authorities, such as the giant Bonneville system in Washington state.

The action came as the Senate began consideration of its $3.9 billion version of a wrap-up appropriations bill for the fiscal year ending Sept. 30, including funds for everything from defense to farm subsidies. Individual items include $13 million for still-to-be determined security measures at the Capitol, $660 million for enhanced security at U.S. embassies abroad, $526 million for space shuttle repairs and $150 million in new military and economic aid to the Philippines. There is even $200,000 to encourage rapid flight of blackbirds through sunflower-growing regions.

As the Senate met past midnight on the spending measure, it rejected an effort by influential senators to earmark $80.6 million in defense funding for 11 of the senators' favored universities, although supporters of the earmarking contended that the action would only strengthen the hand of the House in insisting on contracts for its pet colleges.

Earlier, the Senate also refused to consider lowering the limit on income that senators may earn from outside speechmaking from 40 percent to 30 percent of their $75,100 salary. The proposal to reduce the honorarium limit, made by Sen. William Proxmire (D-Wis.), was defeated on a procedural vote of 68 to 30.

The two regional power issues were highly important to the administration in different ways.

The administration singled out the rural electrification proposal for special criticism in its review of the legislation. It would benefit "one class of borrowers . . . at the expense of the general taxpayer," said the administration in a statement, by allowing refinancing of high-interest government loans at lower rates on the private market, with the government absorbing the difference in cost.

It also objected to another provision in the same section of the bill that would allow farmers who are unable to plant crops because of floods and heavy rains, many of whom are in the upper Midwest, to keep their advance deficiency payments if their farms are in designated disaster areas.

Sale of the power-marketing authorities had been a key element in administration plan to sell off a variety of government assets as part of the "privatization" of government commercial activities, one of the hallmarks of its budget plan for fiscal 1987. It estimated sale of the Bonneville authority and four other smaller ones would save the government $12.7 billion over five years.

But the idea struck Republicans from the region as tantamount to sale of its crown jewels.

"A ludicrous proposal that ought not to go anywhere and will not go anywhere," fumed Sen. Daniel J. Evans (R-Wash.) about a move by Sen. Gordon J. Humphrey (R-N.H.) to allow expenditure of funds to continue studying the idea. "Ill-intentioned," said Gorton, speaking of the administration plan.

Republicans who joined Gorton and Evans in opposing continued funding of efforts to sell off the power authorities included several from the region who normally support the administration on domestic spending cutbacks. Among them was Sen. Steve Symms (R-Idaho), who is in a difficult reelection fight this year.

Together, the Midwest and Northwest, especially the economically distressed rural heartland of the country, have enough Republicans in tight reelection fights this fall to tip control of the Senate, which the GOP now controls by a 53-to-47 vote margin.

Critics of the treatment accorded the two regions were particularly scathing in their reference to the rural electrification loan bailout. Sen. Phil Gramm (R-Tex.), who led the fight against it, called it a "gigantic ripoff of the American public . . . pork-barrel that would give the whole nation trichinosis." But Gramm fared little better than Humphrey. Gramm lost on a 62 to 37 vote challenging the loan provision's germaneness to the bill. Humphrey lost, 73 to 25.