This sentence sounds like informal, spoken English. I would make some slight changes to yield the following: I was told that I would need to substitute for you until September 25th, which means that they are all yours starting tomorrow. This sentence makes sense if today is September 25th. I imagine that one teacher, who was acting as a substitute teacher, is speaking to the returning, regular teacher on September 25th. The substitute teacher is saying "the students are your responsibility (once again), starting tomorrow."

The “they are all yours” is very good colloquial English. To say what you want you just need to add a “for” to change it to “...substitute for you...” Also I thought till was incorrect there, but I looked it up and it is correct as a slightly informal way of saying until.

yep this sentence is correct

I've been substituting my colleague for 3 weeks and now she is asking me if she should return to her group. This is my answer and I kinda wanted to make a joke that they are yours. I'm not sure if did it right.

“Substitute you” is unclear. It appears someone is going to do something in your place. Can you give us more context, or information about the situation?