Kok, who has occupied the role since December 1997, helped the club to seven S.League titles and three Singapore Cups and was known to be regarded as a "mentor and role model to the staff, coaches and players".
In a statement released by the Warriors on Friday, it was announced that he will be replaced by Chong, who has been involved in sports management throughout his career.
In a moving parting speech, Kok, who will be taking over as the S.League's director of operations, paid tribute to all involved with the club and was looking forward to contributing further to the country's football scene.
"It has been a thoroughly satisfying and rewarding time I had at SAFFC and the successes would not have been possible without strong support from the management, my colleagues and the team, not forgetting the fans," Kok said.
"But, it is time to move on and, as I bid farewell to the Warriors, I am looking forward to [contributing] more to the S.League and Singapore football in what is possibly the final phase of my working career."
Club chairman BG Lam Shiu Tong paid tribute to the effort Kok had put in over the years.
"SAFFC [are] indebted to Wai Leong's dedication, commitment and sacrifices for the club," Lam said. "On behalf of all members of the SAFFC management committee, staff, coaches and players, we thank Wai Leong and wish him success in his future appointment as Director of Operations, S.League.
"It is believed Wai Leong will continue his passion and devotion in developing local football to another level of excellence."
Not willing to rest on the club's laurels, Chong has already set his sights on leading the club onwards.
"I am definitely looking forward to my new role and sharing the best of my knowledge and passion in football to drive the club to greater heights," Chong said.
Chong's first match as SAFFC general manager will be on Sunday, when the Warriors take on Harimau Muda at the Choa Chu Kang Stadium.