I also use Matlab to edit and create models before I run them in Abaqus. I've found two ways of doing what you mentioned. The first was to use Matlab to write a python script around the mesh values, then execute that paython script in ABAQUS from the matlab command line (or as last line of the script). That then starts CAE, generates the sketches, and makes model parts from them. Then work from there inside CAE. In this case, I usually called the ABAQUS meshing tool from python instead of supplying the mesh directly.
The other is to use Matlab to write the .inp file directly (the syntax isn't that complicated, at least for the geometry parts). Then you can import the model into CAE using the "import from input file" option, with the finished mesh and everything.