In a statement, the man known as "Mr Chip" said the time had come to "start anew with new spirit and young leadership".
The "crisis" alluded to in the letter has largely been read as a reference to the imprisonment of Samsung's de facto leader Lee Jae-yong on bribery and corruption charges. But it also announced the resignation of a key executive, Kwon Oh-hyu.
Lee's father, Lee Kun-hee, who still retains the chairman title, has been bedridden since 2014 due to health problems, and Lee Jae-yong was sentenced to five years in prison in August for bribing former President Park Geun-hye.
Friday's personnel announcement came shortly after the company said it was expecting to log 14.5 trillion won ($12.8 billion) in operating profits for the July-September quarter, an all-time record and almost three times the 5.2 trillion won of the same period a year earlier.
His departure from office Oh-Hyun Kwon explained, "an unprecedented crisis", saying that the company in the current environment should lead to new leadership.
However, in a sign of good news for the company, its estimated operating profits for the third quarter of 14.5 trillion won (US$12.8 billion) marked a record for quarterly profit, almost tripling the 5.2 trillion won earned a year earlier.
"[Samsung] has been showing record performances", Kwon said.
He added, the company is making record earnings, which are consequences of decisions and investments from the past.
It is noted that Samsung has long had serious problems.
The release of new models, including the iPhone X by rival Apple Inc could weigh on Samsung's mobile sales, but will also help its smartphones parts business, Mirae Asset Daewoo Securities Co analyst Doh Hyun-woo said in a report.
Kwon will leave the company in March, when his term as chairman of Samsung Electronics ends.
He played a major role in strengthening Samsung Electronics' position in the memory chips business across the world.
In its earnings preview on Friday, Samsung put its July-September operating profit at 14.5 trillion won ($12.8 billion), compared with 5.2 trillion won ($4.6 billion) a year earlier.