I created several simple ggplot2 plots and saved them to PDF files using the following commands:
p <- ggplot(plotobject, aes(x=Pos, y=Pval),res=300) ggsav
You can download the font AdobePiStd - just Google it, download and install. After you reboot, the font should display correctly. You can then use the 'Find Font ...' utility within Illustrator to change it if you wish.