Toney was capped by Southgate for the first time in March, while betting charges were hanging over the 27-year-old.
He will not even be allowed to train with his teammates until the halfway point of his ban is up in September.
An independent regulatory commission imposed the sanctions after Toney admitted to 232 breaches of gambling on football.
Players are banned from betting even on matches they are not involved in.
"I have spoken with him. I don’t know if that’s allowed, by the way. If it isn’t then they can ban me and not add to his," said Southgate as he announced his squad for Euro 2024 qualifiers against Malta and North Macedonia next month.
"Look, the ban is the ban. It is what it is. I think he recognised and accepted the punishment. What bothers me is we’ve got to look after people.
"He’s injured at the moment, what does he do about getting fit? How do we give him some structure over the next few months that he can develop himself or be a better person at the end of it or have experiences that he might not experience?
"I don’t like the idea that we just leave somebody so they are not allowed to be a part of the football community.
"I don’t think that’s how we should work, I don’t think that’s how the best rehabilitation programmes would work."
