This uses git's internal difftool. Maybe a little work to do but straight forward.
#First checkout the branch you want to merge into
git checkout <branch_to_merge_into>
#Then checkout the file from the branch you want to merge from
git checkout <branch_to_merge_from> -- <file>
#Then you have to unstage that file to be able to use difftool
git reset HEAD <file>
#Now use difftool to chose which lines to keep. Click on the mergebutton in difftool
git difftool
#Save the file in difftool and you should be done.