All 12 to 15-year-olds will also be offered a single dose from next week, in a “significant, and very welcome” extension of the vaccination programme announced by Nicola Sturgeon on Tuesday.
The first nine vaccine priority groups will be eligible for a booster jag, including over 50s, frontline health and social care workers, and all those over 16 with an underlying health condition.
Care home residents will be given both flu vaccines and Covid booster jags from next week, while from Monday frontline health and social care workers will be able to book their third dose.
Drop-in vaccination centres for 12 to 15-year-olds will also open from Monday, with invitation letters sent out the following week.
Shortly after this, all over 70s and those over 16 at the highest risk from Covid will be contacted by letter or through their GP.
The remaining groups eligible for a booster will be able to book from October.
Booster jags will be given no earlier than six months after the second dose.
Most will be Pfizer, regardless of the type of vaccine someone received as their first two doses.
A half dose of Moderna will also be used as an alternative, again regardless of the vaccine received previously.
The AstraZeneca vaccine has also been approved as a booster, but the JCVI said had chosen Pfizer and Moderna for preference as they are mRNA vaccines.
Professor Wei Shen Lim of the JCVI said the recommendation was based on clinical trial data, including the UK’s Cov-Boost study.
The Pfizer jag is “well-tolerated and has a good effect” he said.
Prof Lim added that it has been deemed safe for people to be given a flu vaccine and Covid-19 vaccine at the same time.
But contrary to previous interim advice, booster Covid vaccines will not be offered to those at higher risk from flu but not Covid-19.
As with older children, those aged 12 to 15 will be offered a single dose of Pfizer vaccine.
Parents or carers will be invited to accompany children to their appointment, with an opportunity to ask questions and discuss concerns, the First Minister said.
The planned rollout to under 16s has been supported by the Royal College of Paediatrics and Child Health.
"We believe that vaccination could benefit healthy children, irrespective of any direct health benefit, in enabling them to have less interruption to school attendance, to allow them to mix more freely with their friends, to give more protection to friends and family members whose health may be at risk from the virus, and to help reduce the anxiety some children feel about Covid-19,” the college said in a statement.
Health Secretary Humza Yousaf said: "I recognise the impact disruption to education can have and am keen that we do all we can to reduce this so I am happy to accept the recommendation to proceed.”
After drop-in sessions in the community, anyone in this age group who has not yet had a dose of vaccine will be offered one at school.
Ms Sturgeon told MSPs on Tuesday: “I know that these are important decisions for young people and their parents, and that many will have questions.
"I would encourage everyone to read the information that will be provided, and do not hesitate to visit a drop in clinic to ask any questions or raise any concerns.
“Vaccination is a vital part of our overall protection against this virus. That is why it is important to support people - especially young people - to make informed choices that they feel comfortable with.”
She added: “In addition to the CMO advice on 12 - 15 years olds, we have received today the final JCVI advice on a vaccine booster programme.
“This is in addition to the third doses already being offered to people who were severely immunosuppressed or immunocompromised at the time of their first or second vaccination.
“I can confirm that the Scottish Government is also accepting this advice.
"The booster programme is intended to prolong the protection that vaccines provide against severe Covid illness.
"It will run alongside our biggest ever flu vaccination programme – since both of these programmes are important for individual and public health.
"Wherever possible, eligible people will be offered Covid-19 and flu vaccines together.”
Scottish Conservative leader Douglas Ross said the booster and teen vaccine programmes have “the potential to be game-changing in halting the spread of Covid this winter”.
He called for mobile vaccination units at every school “to encourage uptake, particularly those in areas where vaccination rates are low”.
Labour leader Anas Sarwar called on the government to ensure all teenagers wishing to be vaccinated are able to receive a dose by the start of the October school holiday.
The Scottish Greens said Scotland must play “catch up” with teen vaccinations.
Health spokesperson Gillian Mackay said: “Millions of children around the world have already been vaccinated and the UK is significantly behind other countries in its rollout to young people.
"It’s important young people and their parents have full confidence in the vaccine and are encouraged to take it up.”
Ms Sturgeon announced the changes to the vaccination campaign as she said that Covid cases in Scotland, while still at a high level, were "starting to fall slightly”.
There were 3,375 positive cases reported on Monday, while the number of people in hospital with the virus has risen by 16 to 1,064, with 89 people in intensive care.
A further 21 new deaths have been reported amongst people who were confirmed as having Covid in the past 28 days – with this taking the total under this measurement to 8,263.