Pierre Wauthier, who had served as the company's chief financial officer since 2011, was found dead at his home on Monday.
The following day police said that he probably committed suicide.
"The unexpected death of Pierre Wauthier has deeply shocked me," explained exiting board chairman Josef Ackermann, a former head of Deutsche Bank.
"I have reasons to believe that the family is of the opinion that I should take my share of responsibility, as unfounded as any allegations might be," he said in a statement.
Therefore, he had decided to resign "to avoid any damage to Zurich's reputation," he said.
The insurer's board said it had accepted his decision "with deep regret," and announced that vice-chairman Tom de Swaan would take his place.
Ackerman's term as chairman was set to expire in 2015.
A graduate of the University of St. Gallen, where he earned a doctorate, he only joined Zurich Insurance in March last year following a stint as CEO at Deutsche Bank.