It will depend on what you need.
Yaris is more economical, and that combined with lower token tax and cheaper maintenance (also under warranty since it will be new), the cost of ownership will be lower. And it is a comfortable car, rear space is a little less, and the sloping roof is a less headroom issue for tall people in the rear seat, but should be more space than Honda City that you are currently using.
Civic is one category higher than Yaris, it has better drive, more space, and more powerful 1800cc engine. If you drive it economically it should give decent mileage too, but not as good as Yaris.
It is not possible to directly compare the two cars, so the decision comes down to what you prefer and what drawbacks you are willing to accept.
