Can I put the editor in the Acknowledgements? I am currently having an exceptionally good and fair editorial process with a paper.

One of the two reviewers suggested a rejection (still providing many suggestions for improving the manuscript). 

The editor was able to understand that many issues raised by the reviewer were because of how the paper was written instead of the actual research design and the results of the study. Additionally, the editor was also able to understand that the study is multidisciplinary and that some issues were born on the side of the non-familiar discipline for us (both the editor and the reviewers are expert in this discipline). These issues were not severe but quite a few.

Instead of rejecting the article, the editor requested major revisions and actually provided substantial suggestions for improving the manuscript. Exactly how the reviewers did. 

I revised the manuscript and acknowledged the "help of two anonymous reviewers". However, this time I truly feel that I should thank the editor, as well. I have never seen this in a paper. Is there a reason for that? Can I acknowledge the editor in my paper?
There is nothing wrong with acknowledging an editor that goes beyond what can be expected. It is of course not customary to provide such acknowledgement in most cases. Editors do not expect it and it may simply appear as inappropriate attempts at flattery. It is difficult to draw the line where acknowledgements are appropriate but, I have probably acknowledged editors in a couple of percent of my own papers. I have also been acknowledged a couple of times in my capacity as editor (out of editing hundreds of papers), all in cases where I have felt my assistance would save a paper that could otherwise be buried undeservedly. In any case, your description seems to fit a case where the acknowledgement is appropriate, although no editor would probably expect it.