If I understand this correctly, you experience an unintended camera shake on a time lapse clip? Is this a video clip or a series of photos?
If the first, you can simply apply the Warp Stabilizer effect on the clip. But, depending on the shake, this may result in severe cropping, so you can also consider editing out that portion of the clip, assuming that the camera came back to its original position.
If the latter, I have found that After Effects is far more powerful in dealing with this. In this app, create a composition that will contain the original picture sizes (e.g. 5K). Drag this comp into a new comp that matches the desired resolution (e.g. 4K) and apply Warp Stabilizer. While super-imposing AE on top of PPro, drag the Comp from AE to PPro to create a dynamic link between both apps.