In a letter to the staff, Samsung CEO said, "As we are confronted with unprecedented crisis inside out, I believe that time has now come for the company start anew, with a new spirit and young leadership to better respond to challenges arising from the rapidly changing IT industry".
Analysts said Samsung's chip business may have posted an operating profit of 10 trillion won in the third quarter, along with sales of 20 trillion won, putting the operating margin at above 50 per cent.
The Samsung CEO said he is so proud to have contributed in developing Samsung as one of the most valuable companies in the world.
Meanwhile, according to commentators, the surprise resignation of Samsung's chip and display head came amid expectations he would take on bigger roles following Lee's arrest in February and the departures of other key executives in the wake of the bribery scandal.
Mr Kwon said he had been thinking about his departure "for quite some time" and could "no longer put it off". Vice Chairman Oh-Hyun Kwon announced his intention to leave the company - including stepping down from his position on the Board of Directors - today.
Further, Chung Sun-sup, head of the corporate analysis firm chaebul.com, said that Kwon had been the face of the company ever since the company had been engulfed in legal troubles.
The 60 company strong Samsung conglomerate it undoubtedly weathering a severe management crisis. In August, Samsung Vice Chairman Jay Y. Lee was sentenced to five years in jail after being guilty of bribery, embezzlement and perjury charges.More news: Gabrielle Union, Kerry Washington Join Twitter Boycott Over Rose McGowan's Suspension
Mr Lee was accused of giving donations worth 41bn won ($36m; £29m) to non-profit foundations operated by Choi Soon-sil, a friend of South Korea's former President Park Geun-hye, in return for political favours.
However, the leadership troubles do not appear to have hit the company's bottom line yet.
Mr Kwon - affectionately known as "Mr Chip" - has been with the company for 32 years, and chief executive of Samsung's hugely successful components business since 2012.
His Samsung Electronics stake, albeit below one percent, is now worth 2.3 trillion won ($2.03 billion).
While memory chips were the main driver of Samsung's profits, its mobile phone business was given a boost by its new Note 8 smartphone which received the firm's highest number of pre-orders.
"The shipment of DRAM and NAND products increased 12 percent and 21 percent (in the July-September period) on-quarter, while the average sales price also advanced 6 percent and 2 percent, respectively", said Kim Dong-won, an analyst at KB Securities Co.