The money so received from sale of flat will have to be divided in 2 parts, one for you and the other for your brother. Unfortunately, in this transaction, he cannot avoid taxation. He will have to pay whatever taxes come in his hands and file a tax return. You are advised to transfer the amount of taxes leviable on him on account of such capital gains given that you have received full payment from the sale.
CG account is opened for saving capital gains tax by investing in a new house u/s 54, of ITA. Since you are purchasing the new house, i assume you have taken care of this fact and you are saving the capital gains tax. In order to save the capital gains in your brother's hands, his name must continue as a joint owner in the new property and naturally his name would have to be included in the CG account as well.
If he cannot be an owner in the new house, then he cannot avail that exemption of CG tax and hence you will be advised to remit him the amount of CG tax so that he can pay that.