But they'll remain in custody until concerns for community and family safety can be addressed.
The boys, aged 16 and 17, were arrested on Wednesday, more than a week after Mr Mohamed's stabbing death.
His body was discovered on St Kilda beach after an altercation on December 4.
They faced a children's court for a bail application. Each is charged with affray and violent disorder.
The court heard Youth Justice could put a plan in place to support the boys on bail, but that it would take some time and involve meetings with Victoria Police about how to minimise risk to the community and their families.
A worker who assessed one of the boys cited "concerns regarding conflict in the community with two peer groups" while another said freeing them on bail would be premature.
A homicide detective told the court several other people are still to be arrested and interviewed in connection with the incident.
Lawyers for the 17-year-old boy, who is from Taylors Hill, said risks could be mitigated by having him go to work with his mother each day, not associate with others and to stay away from St Kilda.
The 16-year-old, from Kurunjang, was supported in court by his mother and brother.
The magistrate indicated he was concerned about risk and wasn't prepared to release either of them on bail without a plan in place.
But he gave Youth Justice a week to come up with something, indicating if that was done he would free them.
Their case will return to court on December 22.
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