The bitter 90-day strike by nurses in La Plata, Md., ended early yesterday as weary negotiators approved a new two-year contract with Physicians Memorial Hospital.

"It is a new beginning," said Theresa H. Boone, president of the Physicians Memorial Hospital Staff Nurses Association, who added that she expects most of the 63 striking nurses back on the job by week's end.

The two-year contract gives the nurses a 9 percent wage increase this year and a 7 percent raise in 1984, plus 2 percent increases each year on the anniversary of a nurse's employment. At the same time, the nurses agreed to cuts in the amount of leave time they can accrue.

"It's a settlement that I am happy with," Boone said.

"The final settlement represents a resolution . . . that is fair and equitable to both sides," said hospital attorney John G. Kruchko. Another hospital lawyer said that, in a separate return-to-work agreement, the hospital will recall the nurses to their jobs as soon as they are needed.

Boone said that because the hospital has been shorthanded, she expects most nurses will be back to work by the end of the week as admissions limits are lifted and physicians begin sending more patients.

Boone also said the agreement included a clause promising there will be no retaliation against the strikers, who made up about two-thirds of the small hospital's normal complement of nearly 100 nurses.

The nurses' old contract ran out in June, and disagreements on wages and benefits led to the Nov. 3 walkout.

The nurses set up a picket line, staged candlelight vigils and leveled angry charges that the hospital was letting the strike run so long in an effort to break the union. Those charges were denied by the hospital, which continued to operate by using temporary and part-time nurses.