Ms Green has been handed 4.1 million shares - the bottom end of the range to which she is entitled - after meeting financial targets during her two and a half years at the helm of the group.
She will give around £1.9 million to charity after intense scrutiny of the company’s response to the deaths of Christi and Bobby Shepherd by carbon monoxide poisoning in 2006.
The charities have been chosen in consultation with the parents of Christi and Bobby, Thomas Cook said.
The group said a “substantial” donation would be made to a carbon monoxide charity to support the work of the recently launched joint initiative with Thomas Cook to fund research into protection from carbon monoxide, limit the risks associated with it and raise general awareness of the related dangers.
The parents of Christi and Bobby have “expressed their satisfaction with this outcome”, added Thomas Cook.
Ms Green’s pay award has attracted controversy given her role in charge of the group at the time of the tragedy.
Bobby and Christi, aged six and seven, from Horbury, near Wakefield, died at the Louis Corcyra Beach Hotel on the Greek holiday island when they were overcome by fumes from a faulty boiler.
An inquest in May ruled that the children had been unlawfully killed and concluded that travel firm Thomas Cook breached its duty of care to the family.
Peter Fankhauser, who succeeded Ms Green as chief executive of Thomas Cook last November, has admitted the travel giant failed in its handling of the tragedy and pledged to help the children’s parents move on with their lives.
Thomas Cook said Ms Green’s shares bonus was based on business performance, including share price, adding the group’s stock price rose from 16.25p to 136p during her time in charge.
She could have been in line for a much bigger share award of up to 7.1 million shares under the plan.
The group announced Ms Green’s shock departure last November, although she has since been on gardening leave until her employment at the group officially ended today.
She joined the company from Leeds-based technology distributor Premier Farnell, where she was chief executive.
Last month, the children’s mother accused Ms Green of trying to use their memory to gain public sympathy.
Sharon Wood told a London press conference: “If Harriet Green feels the need to offload some of that money to salve her conscience, that is her decision to make, but to try and gain public empathy by attaching her donation to the memory of my Christi and Bobby I find abhorrent.”
Ms Green Thomas Cook from July 2012 until November 2014.
An angry Ms Wood suggested that Thomas Cook should “reconsider” handing out the bonus because the success of a family-friendly company should not just be about money and share prices.
“It must also consider the well-being and safety of its customers whilst on holiday and the way they are subsequently treated,” she said.
The size of Ms Green’s bonus is “a matter for her own conscience”, according to Ms Wood.
She added: “We believe that when she took the helm she did not move the company on with sensitivity towards us as a family.
“If the company’s brand has suffered, those at the top of the organisation must accept responsibility in relation to the decisions made over the handling of us as a bereaved family.”
She flatly denied that the children’s father had received a letter offering a meeting with Ms Green.
In fact he has still not had a response from her despite writing to her on at least five occasions since July 2013, Ms Wood said last month.
She added: “As for me, Harriet Green has never had the humanity or compassion to write to me as the bereaved mother of Christi and Bobby and, as far as I am aware, she makes no claim to having done this.
“I would have liked to have met with Harriet Green this week but I have been told that she is out of the country.”