Coping stone mismatch on corner of roof causing water damage to my wall
I'm guessing that the root of the issue isn't so much the joint as the drainage profile being wrong. It looks like the greenhouse was a later addition on what used to be an open deck (that would have been sealed and drained either with a floor drain or scuppers.  The cement capping on the top of the wall is crowned, but the greenhouse walls are attached below the crown.  This basically makes a water trap for anything that runs down the glass, and is exacerbated by the lack of gutters on the greenhouse.  The crack between the caps is just the most convenient place for it to have failed, but it has probably been begging to leak since it was installed.

I'd do one of 2 things (in addition to repairing the mortar joints) - either put a gutter at the bottom of the glass with a drip edge running into it (probably cheaper and easier)...



...or have a metal cap made to correct for the improper placement of the greenhouse walls (likely more expensive but would look a lot better):



Neither of these solutions are ideal, but without removing the greenhouse and re-capping the wall your options are a bit limited.