Both have since left the automaker.
The suit was filed in May by Sayaka Kobayashi, who sought nearly $200 million in damages.
Ms. Kobayashi had worked as an assistant to Hideaki Otaka, who served until May as president and chief executive of Toyota Motor North America, which oversees the company’s manufacturing and financial operations from New York.
Terms of the settlement, announced in a joint statement by Toyota and lawyers for Ms. Kobayashi, were not disclosed.
“We are very pleased to have resolved this matter in a way that all parties have agreed is fair, appropriate and mutually satisfactory to all concerned,” the statement said.
A spokesman for Toyota, Steven Curtis, declined to say whether the company paid Ms. Kobayashi as part of the settlement.
Mr. Curtis said Ms. Kobayashi had “made a personal decision to leave Toyota to pursue other interests.”
Mr. Otaka, who had been scheduled to be reassigned to a job in Japan, has retired from Toyota, Mr. Curtis said, but declined to comment further.
A lawyer for Ms. Kobayashi could not be reached.
Mr. Otaka went on leave in May after Ms. Kobayashi filed her complaint in State Superior Court in Manhattan. In the lawsuit, Ms. Kobayashi, 42, accused Mr. Otaka, 64, of making repeated unwanted sexual advances.
She said Mr. Otaka arranged her travel and office schedules so that they would be alone together, required her to accompany him to social functions and groped her at a Washington hotel and in Central Park, which is near Toyota’s New York offices.
When she complained, she said, she was involuntarily transferred to a position in Toyota’s planning department, where she remained after the suit was filed.
Ms. Kobayashi sought at least $40 million in damages for emotional distress and injury to her reputation, as well as $150 million in punitive damages.
Soon after the suit, Toyota formed a special task force, led by Alexis M. Herman, a former secretary of labor for President Bill Clinton, to review Toyota’s policies and procedures on harassment and discrimination. Ms. Herman heads a diversity advisory board at Toyota.