Lee announced in April he was quitting after prosecutors charged him with tax evasion and breach of trust.
The strategic planning office, once seen as the "control tower" of the loose-knit group, was scrapped at the same time.
A seven-member committee led by a Samsung Electronics vice chairman Lee Yoon-Woo will decide on new projects and coordinate investment by subsidiaries to avoid duplication, Samsung said in a statement.
A separate six-member committee will be led by Lee Soon-Dong, president of Cheil Worldwide, an advertising unit of the group. It will be in charge of enhancing Samsung's brand image.
The move is aimed at addressing concerns of a vacuum in decision making.
"With today's changes, the group has completed a management revamp Lee (Kun-Hee) promised earlier," group vice president Yoon Soon-Bong told reporters.
Lee, 66, had been at the group's helm for two decades and is now on trial.
The tax evasion charge relates to the alleged hiding of assets in borrowed-name accounts. The breach of trust charge concerns the transfer of management control to his 39-year-old son Lee Jae-Yong through a convertible bond issue.
The strategic planning office, a group of some 90 officials, was seen as being at the centre of the accusations.
In court appearances Lee has apologised for any lapses but has denied the substance of the charges.
