Cole Gibson, seven, and Michael Joyce, 31, were passengers in a northbound silver Renault Kangoo which was in a collision with a southbound Peugeot north of Bankfoot at about 7:30pm on Friday.
Pregnant Hazel Gibson, 29, from Lochgelly in Fife, was driving the Kangoo and sustained serious injuries in the crash, including a fractured collarbone, back and pelvic bone. Her 17- week-old unborn baby survived.
Mr Joyce of Canongate, Edinburgh was the front-seat passenger and was pronounced dead at the scene.
Cole was taken by ambulance to Ninewells Hospital in Dundee, where he died on Sunday as a result of his injuries.
Ms Gibson said it was her son’s decision to join the organ donor register.
She said: “Cole decided he wanted to be on the organ donor register when he was five years old, after he picked up a leaflet that came through the letterbox.
“We made a decision then as a family that it was what we all wanted to do and we are now all on the organ donor register.
“Knowing that Cole’s death is helping other children waiting for life-saving transplants is helping me in some way to come to terms with what has happened.
“I already know that his heart is going to a two-year-old girl and that has given me a glimmer of hope knowing that whilst he is not here, he’s still making a difference to a very sick young girl elsewhere in the UK.
Ms Gibson also described the fact that she had not miscarried as a “miracle”. She said: “I can only think that wearing a special pregnancy bump seatbelt helped in some way, although I can never be sure.”
Ms Gibson added: “I just hope that when people read this they will appreciate how precious the gift of life can be and to consider putting themselves on the organ donor register.
“I know it’s not for everyone but if a few more join as a result of what has happened to my family, then Cole’s death has not been in vain.”
Cole was a Primary 3 pupil at Benarty Primary School near Lochgelly, in Fife.
Head teacher Eleanor MacGregor said: “Cole’s sudden passing has come as a great shock to the whole school community.
“A lovely, friendly boy, Cole was very popular with all staff and pupils across the school and we will miss him terribly.”
Two women, aged 18 and 19, who were in the other car involved in the crash were taken to hospital with minor injuries, but have since been discharged.
The A9 claimed 13 lives in 2010, a toll that prompted more than 10,000 people to sign an online petition to have the road fully dualled.