Garfinckel, Brooks Brothers, Miller & Rhoads Inc. was acquired by Allied Stores Corp. of New York yesterday, and Garfinckel Chairman David R. Waters quit soon afterward.

The Garfinckel corporation's 75-year history as a Washington retailer ended with a perfunctory vote to merge with a subsidiary of Allied.

The merger was effective at the close of business yesterday, incorporating the various Garfinckel retail operations into two new divisions of Allied.

The acquisition of Garfinckel's for $235 million makes Allied Stores the nation's 10th-largest retail chain.

Waters, who refused to discuss his plans during the morning meeting, announced his resignation later in the day.

Waters' decision was not unexpected. He had fought the takeover aggressively, criticizing Allied Chairman Thomas Macioce in language that made it unlikely the two would ever work in tandem.

"If you'd been a little more subtle with Mr. Macioce he might have offered you the presidency of Allied ," stockholder Eveyln Y. Davis chided Waters during the morning meeting.

"You know I'm not subtle," Waters responded.

Waters declined to comment on suggestions by Davis that he is being considered for two top management jobs at Associated Dry Goods, the parent of Lord & Taylor, and Marshall Field & Co., the big Chicago department store chain.

Allied issued a statement saying it had not asked for Waters' resignation, quoting Macioce as saying, "Mr. Waters led a senior management team that built the company into one of the finest diversified specialty retailers in the country."

Allied officials said there is no immediate plan to replace Waters, whose job becomes largely superfluous under the new table of organization drawn by Allied for the diversified Garfinckel operations.

Allied had said earlier that Waters would be put in charge of a specialty store division including Garfinckel's, Brooks Brothers, Ann Taylor and Catherine's Stout Shoppes; chief executives of those chains will now report directly to Macioce, as do the heads of the other store groups owned by Allied.

The other Garfinckel retail divisions--Miller & Rhoads of Richmond, Millers of Knoxville, Tenn., and Harzfeld's Inc. of Kansas City--will become part of a department store division headed by former Garfinckel President Manuel Rosenberg.

No other Garfinckel executives indicated immediately that they planned to leave the company. Allied has said it will keep open Garfinckel corporate offices here.

The retail store started by Julius Garfinckel in 1905 grew into one of the nation's most successful specialty retailers over its 76-year corporate life.

The company's biggest problem was the Miller & Rhoads department stores, which were losing money. Garfinckel's was negotiating to sell Miller & Rhoads to Allied when on Aug. 14 the New York chain made a sudden, unwelcome and unexpected offer to buy the entire company.

Waters fought for two weeks, but on Sept. 1 the Garfinckel board gave in and accepted Allied's offer of $53 a share for Garfinckel stock.

By yesterday, Allied had acquired more than 92 percent of the Garfinckel stock, enough to assure an overwhelming victory in stockholders' balloting on merging the two firms. The final tally showed 4.2 million votes for the merger, 7,855 against and 1,293 abstained.