Can I pursue B.Com after completing class 12th in science from Gujarat board?

Yes, you can pursue B.Com after completion of your 12th class from science stream. But you'll need to handle different subjects. Now it's up to you that you can manage it well or not. Visit here for B.Com colleges in Gujarat: https://www.shiksha.com/accounting-commerce/colleges/b-com-colleges-guja

I don't know about eligibility in your case, but having done science till 12th, it's going to be a difficult task for you. I don't mean to demotivate you, but it's the truth. Subjects like accountancy will be challenging for you.