The Sharks claimed their first away win over an Irish province at Thomond Park, ending Munster's unbeaten run in the United Rugby Championship.
Munster fell to a second successive league defeat after the Sharks secured four victories from five fixtures this season.
Gianni Lombard scored the game's only try for South Africa following a kick by Zakhelelo Siyaya that Hanrahan misjudged while covering.
Van Zyl Con also crossed for the visitors, with both tries coming in either half of the match.
Munster registered their sole points when Hanrahan slotted over after struggling to apply pressure in Sharks territory.
A major flashpoint occurred when Ox Nche received a yellow card following contact with Munster replacement prop Jeremy Loughman's head.
Lombard restored the Sharks' five-point lead with a penalty kick before Van Zyl crossed in the 59th minute to seal the result.
Munster head coach Clayton McMillan made seven changes, including a debut for former Leinster wing Rob Russell, but could not overcome the deficit.