(1) Join the 2 separate PDFs into 1 file (e.g. joined.pdf) using tools such as pdfunite, pdfsam or pdfshuffler.
(2) Install pdfjam.
(Note: If you’re using Arch Linux, pdfjam is included in the texlive-bin package)
(3) Use the pdfnup tool from the pdfjam package to merge page 1 and page 2 of joined.pdf into a new pdf file consisting of only a single page, with page 1 stacked on top of page 2:
$ pdfnup joined.pdf --nup 1x2