The United States and Canada exchanged diplomatic notes and President Reagan telephoned Prime Minister Brian Mulroney Saturday in the relatively quiet culmination of a two-year battle over the most comprehensive trade pact ever between the two countries.

The U.S.-Canada free trade agreement was to automatically take effect at midnight with the immediate elimination of duties on a wide range of products.Thomas Niles, the United States ambassador to Canada, prepared a diplomatic letter to the External Affairs Department in Ottawa stating the United States is ready to put the trade pact into effect Jan. 1. A representative of the Canadian government delivered a similar letter to the State Department in Washington late Friday.

President Reagan, vacationing in Palm Springs, Calif., telephoned Mulroney Saturday morning in Florida, where the Canadian leader is vacationing, to congratulate him on the final approval of the historic bilateral agreement.

"Together," Reagan said, "our governments have set an example for the world on how eliminating trade barriers can benefit all peoples."

The Conservative Canadian prime minister, who staked his political career on the free trade agreement, issued no statement about it Saturday.

The most immediate effect of the free trade agreement will be the elimination of duties on a broad range of products, including computers, furs, fresh frozen fish, animal feed and whisky.

Duties on all other items traded between the two countries will be phased out gradually over the next ten years.

Canadian officials said consumers will save on purchases of American or Canadian-made products only if the reduced duties are passed on at the retail level.

The acrimonious debate that surrounded the free trade negotiations has faded to a whisper, and only one organization opposed to the agreement planned a protest Sunday in Ottawa.

Pam Chappell, spokesperson for the Canadian Embassy in Washington, said in an interview the implementation of free trade would be surprisingly quiet considering the emotional debate over the treaty in the past two years.

"All the work has been done. All the bridges have been crossed. The agreement has been signed, sealed and delivered," she said.