The State Department yesterday announced a realignment of its Bureau of Near Eastern and South Asian Affairs that appears intended to provide better management of U.S. relations with the region covering Saudia Arabia, Iran, Afghanistan and Pakistan.

However, department officials denied a report in yesterday's Washington Post that Deputy Secretary of State Warren M. Christopher ordered the ouster of two senior bureau officials with only perfunctory notice to Assistant Secretary Harold Saunders.

Yesterday's announcement confirmed that two of Saunder's deputy assistant secretaries - William R. Crawford and Jack C. Miklos - are leaving their posts.

But department officials said the personnel changes were part of a planned restructuring of the bureau's management setup in which Saunders had participated fully. The officials added that Crawford is retiring from the Foreign Service after almost 30 years to enter private industry and that Miklos, who is shortly to be given a new post, was due for regular reassignment.

These officials also said that Christopher routinely signed the order for the changes in his role as acting secretary during Secretary of State Cyrus R. Vance's absence. But they denied that the departure of either official had been forced by Christopher or Vance.

The principal structural change, according to the officials, will be to increase from four to five the deputy assistant secretaries working under Saunders. They said the aim is to increase the number of senior-level personnel concentrating on an area that is a vital source of U.S. oil imports and that has been undergoing considerable upheaval.

Under the new setup, Crawford will be replaced as Saunders' principal deputy by Peter Constable, a career officer with extensive experience in the area. Miklos, who has been responsible for overseeing South Asian policy, will be succeeded by Jane Coon, former head of the office of Pakistan, Afghanistan and Bangladesh affairs.

In addition, Joseph W. Twinam, director of the office of Arabian Peninsula affairs, will become a deputy assistant secretary concentrating on economic and oil matters.

Two other deputy assistant secretaries who have dealt primarily with Arab-Israeli affairs - Michael E. Sterner and Morris Draper - will remain in their posts.