At Windsor Park, Northern Ireland went into the game knowing that a win could put them top of the group. However, the visitors took the lead in the 15th minute through Stanislav Sestak who tapped in a cross.
Filip Holosko scored the second and final goal of the game in the 67th minute before Clingan, who was cautioned in the 17th minute, was replaced three minutes later by Chris Baird.
Former City keeper Jonny Tuffey was a substitute not used whilst former City striker Michael Mifsud played for Malta in a 1-0 defeat to Sweden.
A good number of City supporters were at Wembley to see England book their place at South Africa 2010 with a 5-1 victory over Croatia.
Scotland won't be going after losing 1-0 to Holland. Former Sky Blue Gary Caldwell was on the bench.
Already out Wales were beaten 3-1 at home by Russia.