Your question is very similar to Different infill in the same part and Using multiple infill types within one model [duplicate]. The difference is that you specifically ask for Slic3r and a variation in layer height infill percentage.
Actually this answer describes using "helper volumes" in Ultimaker Cura to set different properties for certain parts of the model (UPDATE: that answer now includes also Slic3r instructions), but it appears that this answer is very much applicable to Slic3r also. Please read this posting. Quoting from the reference:
Finally, I fired Slic3r up and loaded the main part, then clicked on
Settings... and then hit Load modifier... I loaded the new volume as a
modifier mesh and I applied 100% solid infill...
Secondly, this answer where 2 different infill percentage sliced models are manually combined at a certain height may also work for you (this is a perfect valid solution for Slic3r, but requires some editing skills).
Basically, although you request for a solution for a slicer other than already described in other questions, boils down to a similar answer, the only difference is the implementation in Slic3r is called differently.
To do this in Slic3r see this reference.
The blog describes the use of a simple volume (the green volume loaded from an STL file). After loading:
Right-clicking on the main part brought up the object settings menu.
From there, clicking "Load Modifier" and selecting the previously
saved model adds it to the part as a modifier.
The green "+" was selected and "Fill Density" was added to modifier
list and set to 100%.
This shows that the functionality in Slic3r is very similar to the functionality in Ultimaker Cura.