Well, I think using CSS animation is a lot better when there is a supported browser and you should use jQuery only as a backup for unsupported browsers. As thoroughly explained on http://dev.opera.com/articles/view/css3-vs-jquery-animations, they conducted test of animating 300 divs at the same time with both CSS and jQuery, and noticed a huge difference between the performance statistics.
Statistics using CSS the animation were:
- Number of actions performed to finish the animation: 100
- Time taken to finish executing the animation: 2.9 seconds
- Memory consumed at the end of the animation: 1.5 MB
and Statistics using jQuery were:
- Number of actions performed to finish the animation: 2119
- Time taken to finish executing the animation: 5 seconds
- Memory consumed at the end of the animation: 6 MB
So, as you can see, there is a great difference between the performance. This is because the browser's CSS processor is written in C++ and native code executes very fast whereas jQuery (JavaScript) is an interpreted language and the browser can't predict JavaScript ahead in time very well, in terms of what event will occur next, which restricts browsers to optimize it for performance.
I hope that answers your question.