Sale of vehical

Yes. you have to pay tax on profit on sale provided the following condition are satisfied.
1) The vehicle must be capitalised in the business
2) There is no other existing plant & machinery (P&M). Even if there is any plant & machinery, the sale consideration should exceed the entire Written down value of P & M. or
3) The sale value must exceed opening written down value.

No I am asking gst point of view that wheather should I have to pay tax on margin as per cbic notification

No. Capital gain (i.e Margin) is calculated as per income tax provision by considering the above mentioned points. The Gain on which you have changed GST will not be taken into consideration for the purpose of Income tax. Gain ( margin) computation is different in Income Tax Act.