The CGF were initially in talks with Kenya as their preferred host for the meeting, where President Louise Martin will be up for re-election and a host city for the 2026 Commonwealth Games is due to be selected.
The CGF then re-opened the process and both Kenya and Rwanda applied before the deadline of August this year.
Nairobi was set to stage the gathering of the CGF membership pending sign-off from the Kenyan Government, before the organisation allowed other bidders to come forward.
The event is due to take place from September 4 to 8 at the Kigali Convention Centre.
It will mark the 10-year anniversary since the African nation joined the Commonwealth.
"Rwanda’s membership of the Commonwealth is unique and we welcome this opportunity to celebrate and engage with the youngest member of our sporting family," sad Martin.
"They submitted an ambitious, strategic hosting proposal - and see the General Assembly as an important stepping stone for the 2020 Commonwealth Heads of Government meeting.
"Rwanda is an inspiring country with passionate, proactive sports leadership - and we all look forward to ensuring a socially impactful legacy for Rwanda and the host Commonwealth Games Association (CGA) around the shared values and ambitions of Commonwealth sport."
The decision to host the General Assembly in Rwanda comes as part of the CGF's peace and reconciliation efforts.
A minute's silence was held at the Gold Coast Commonwealth Games in April to pay respect to the over one million people killed in the Rwandan genocide.
"We are truly honoured to be selected to host the 2019 CGF General Assembly," Rwanda CGA President Valens Munyabagisha said.
"We want to leverage this important event to build the profile of Rwanda and the wider Commonwealth and also contribute to our shared sporting, social and economic development.
"Our athletes and team will be the proudest of hosts - warmly welcoming the Commonwealth sporting fraternity to Kigali next September.
"Rwanda is increasingly becoming a destination of choice for international meetings, and delegates will see how the capital city of Kigali has come of age: the heart of the emerging Rwandan economy and a pride of every Rwandan."
Rwanda made their Commonwealth Games debut at the 2010 event in New Delhi.
They won their first medal at the Commonwealth Youth Games in the Bahamas in 2017.