The Three Lions had already made certain of their place at next year's World Cup courtesy of a drab victory over Slovenia three days earlier, but Southgate still chose to play the Reds skipper for the full 90 minutes of the dead rubber.
Henderson suffered with heel problems last season, missing the final three months to injury, and Klopp thinks that it was reckless to risk him unnecessarily with the national side.
"England played a friendly game on an artificial surface, it was a qualifying game but they were already qualified," he told reporters today.
"I was not happy that Hendo was on the pitch to be honest with all the problems he's had in the past - I thought it made no sense.
"We cannot be involved in this - they all make their own decisions. No manager of a national side has asked me so far before a game 'How would you line up?'"
Henderson has started all but one of Liverpool's seven Premier League games so far this season and scored the decisive goal in their 3-2 win at Leicester City last month.