Aisha Ilyaas Aden was abducted at a market, raped and strangled to death near her home in Galkayo, Puntland region, in February last year.
Abdifatah Abdirahman Warsame and Abdishakur Mohamed Dige were both shot in Bossasso town square, on Somalia's north coast, after they were found guilty of the shocking attack.
Aisha's father Ilyaas Aden told the BBC he appointed their executioners and asked them for forgiveness by phone before they were killed today.
He even said he walked over to make sure they were dead after viewing the execution.
He is also alleged to have delayed the execution of Warsame's brother, Abdisalam Abdirahman, who had also been found guilty of the crimes, by at least ten days so that his case can be re-evaluated.
The case sparked uproar and demonstrations across the country, and an online protest using #JusticeForAisha.
He attended the execution today with officials and members of the public, reports Mustaqbal radio.
'Sexual violence is sadly not a shocking occurrence in Puntland,' Hawa Aden Mohamed, founder of the Galkayo Education Centre for Peace and Development, which promotes women's rights, said in February. 'For years it has been relatively common place.'
'Aisha's is a truly tragic case, which has resonated very deeply here in Puntland. I hope it will shake things up. The seemingly never-ending violence against women and girls, where men can evade any responsibility for what they do, has to end.'
Somalia's semi-autonomous Puntland region passed the country's first Sexual Offences Law in 2016, which criminalises rape, sexual harassment and online sexual offences.
Under the law, five men who gang raped a teenage girl - with a video of the attack posted on social media - were sentenced in 2017 to lashes and up to 10 years in prison, according to the United Nations.
Campaigners say police are either unaware of violence of women or do not see it as a serious crime, which deters women from reporting abuse.