Safari uses Quartz/Core Graphics for the painting, via OpenGL if applicable. Chrome uses Skia/Ganesh, sometimes via OpenGL--Chrome is more conservative about when it enables the OpenGL-based painting than Safari is, I believe.

If everything else on your machine is slowing down, then chances are good that Safari is hitting some bad case in the way it uses your GPU. CG::OGL may not be optimized well for this use case. (In general retrofitting CPU-based 2D graphics APIs to run on GPUs, as both Chrome and Safari attempt to do, is difficult.) Or the layerization heuristics may be going awry in Safari--unlike Chrome, which does things manually, Safari has a completely different implementation of layers that exports the layer structure of the page to the OS window server.

Though both are on WebKit, they use different renderers. Generally Chrome is better than Safari except on iOS where Apple forces other browser makers to use the Safari engine, I guess it's one way of keeping tabs on mobile browser speed competition :-)