But prosecutors maintained he acted with others in carrying out the attack.
MacAskill controversially released Megrahi on compassionate grounds in 2009 after he was diagnosed with terminal cancer.
The US announced charges against Masud in 2020 and he has now been in custody for two years.
Speaking on Radio’s Good Morning Scotland programme, MacAskill said: “I have always believed he is the bomber.”
On the 36th anniversary of the attack, the acting Alba leader said Mr Masud had “what you might call military skills”.
MacAskill added: “He has returned and will face trial in America, I believe he will be convicted, and he is the bomber.”
He added: “Megrahi himself didn’t have the skills to do so, but that doesn’t mean Megrahi didn’t have a role in the operation.”
