Roberts, the head of trading, magazines and inserts, will leave News International on 2 April, while Rees, the head of News Group, and Gibson, the head of Times Media, will remain at the company until the early summer.
Their roles were three out of four positions placed at risk of redundancy as part of the publisher's move to created integrated sales teams to focus on different audiences, rather than particular titles.
The fourth role, head of Sun digital, which is held by Catherine Frusher, is still under consultation.
The trio who are leaving the company did not apply for four new senior roles, for which a recruitment process is underway.
They new roles are: head of title management; head of news; head of lifestyle, and head of digital. Gibson will perform the head of news role for an interim period and Rees will work as head of title management until he leaves the company.
Karin Seymour, the sales director for NI, said: "During the consultation period we have had comprehensive conversations with all the people currently in those roles.
"As a result of those conversations, I am sorry to announce that Sian Roberts, Lee Gibson and Ian Rees have decided not to apply for the newly created roles and will therefore be leaving NI Commercial.
"Sian, Lee and Ian have agreed to assist in the transition of these roles."