The Senate came within two votes yesterday of pulling the plug on the huge Tennessee-Tombigbee Waterway and slashing money for the Clinch River breeder reactor, as its new budget-cutting zeal was tempered by old-fashioned pork-barrel politics and senatorial courtesies.

Voting 48 to 46, the Senate rejected a proposal by Sens. Charles H. Percy (R-Ill.) and Daniel P. Moynihan (D-N.Y.) to cut $189 million for the waterway project--called a "boon" by its friends and a "boondoggle" by its foes--from a $12.4 billion appropriations bill for water and energy projects.

Then, by the same 48-to-46 vote, it shelved an amendment by Sen. Paul E. Tsongas (D-Mass.) to cripple the $3.2 billion Clinch River project in Tennessee--dear to the heart of Majority Leader Howard H. Baker Jr.--by requiring that private industry pay half the $180 million tab for this year.

So tight was the Clinch River vote that Baker, who has championed budget cuts in other areas, had to pull out all the stops for his home-state project, working the floor intensely to convince reluctant colleagues to go along with him. "It got stolen from us by some persuasion," claimed Sen. Gordon J. Humphrey (R-N.H.).

A final vote on reconsideration will be taken today, but Tsongas, conceding that Baker has more muscle as majority leader than Tsongas has, said it would be "irrelevant."

Also still pending is a Moynihan proposal to make future Tenn-Tom funding contingent on 50-50 financing by states that will be served by the 232-mile barge canal linking the Tennessee River to an existing waterway emptying into the Gulf of Mexico near Mobile, Ala.

Both the Tenn-Tom and Clinch River projects have been supported by President Reagan but have run into mounting opposition from Congress, which is reluctant to shield regional water projects from cuts being imposed on other domestic programs.

In the Tenn-Tom debate, proponents argued that the waterway is 80 percent finished and that any savings from termination of it would pale by comparison with the economic advantages of completion.

Critics, contending that the project will probably cost as much as $3 billion by the time it is finished, said further funding amounts to throwing good money after bad. As much as $2 billion could be saved if the project is ended now, they added.

"A Tinkertoy," claimed Moynihan. An "economic dinosaur," said Percy. "The veritable 'Old Man River' of such capers," argued Sen. Alan K. Simpson (R-Wyo.).

But all the derision that the opposition could muster could not--at least not yet --deflect the powerful currents that run through the Senate when water projects are at stake, especially those championed by the chambers' leaders.

After the vote, Sen. Howell Heflin (D-Ala.), one of Tenn-Tom's advocates, acknowledged that he had used the argument that the reelection chances of Sen. John C. Stennis (D-Miss.) would be enhanced by the project's continued funding.

Moreover, Heflin acknowledged, there was some discussion of other senators' interests in other projects, including the Clinch River reactor.

While he had heard of nothing he would call "trade-offs," Heflin said, "in indirect terms, several projects . . . were mentioned," including the Clinch River project. Added Heflin: "That's nothing new that hasn't happened in the United States Senate since its beginning."

The 48-to-46 vote was the closest that either house of Congress has come to shutting down the 10-year-old Tenn-Tom project, which is expected to cost nearly $2 billion and could cost $3 billion if, as critics suggest, further improvements to the existing waterway south of Demopolis, Ala., are required.

The high-water mark for Tenn-Tom foes in the Senate last year was 36 to 47. Earlier this year, the House only narrowly approved continued funding by a vote of 208 to 198.

But, although the margins keep narrowing, the waterway's opponents keep losing just enough potential supporters so that Tenn-Tom lives on. Asked why several northeastern senators who have no stake in a southern waterway voted for the project, Moynihan cited the Senate's "affection for John Stennis" and noted that "various arrangements" were undoubtedly made. The Senate, added Moynihan, is "legitimately a bargaining institution."

Earlier in the day, the Senate agreed by voice vote to a proposal by Sen. Gary Hart (D-Colo.) to prevent use of spent fuel from nuclear power plants as a source of plutonium for nuclear weapons.

The energy and water bill is $771 million less than a previously approved House version, but exceeds President Reagan's budget targets by $322.1 million.

All Washington area senators voted against continued funding of the Tenn-Tom waterway. They split on the breeder reactor, with Charles McC. Mathias Jr. (R-Md.) and John W. Warner (R-Va.) voting with Baker, and Harry F. Byrd Jr. (Ind.-Va.) and Paul S. Sarbanes (D-Md.) voting against.