The solution depends on the relation between the git ignore rule and the exception rule:
Files/Files in different levels or Files/Subfolders: you can do this:
*.suo
*.user
*.userosscache
*.sln.docstates
# ...
# Exceptions for entire subfolders
!SetupFiles/elasticsearch-5.0.0/**/*
!SetupFiles/filebeat-5.0.0-windows-x86_64/**/*
# Exceptions for files in different levels
!SetupFiles/kibana-5.0.0-windows-x86/**/*.suo
!SetupFiles/logstash-5.0.0/**/*.suo