Marcel Sabitzer scored with a glancing header from Marko Arnautovic's cross in the 75th minute and substitute Martin Harnik added the second in the last minute to leave them four points behind leading pair Serbia and Ireland in Group D.
David Alaba struck the underside of the crossbar in an early attack, leading to a tale of frustration as the ball refused to go in for the hosts.
Arnautovic, Guido Burgstaller and Zlatko Junuzovic all missed chances in the run-up to halftime and it was little different in the second half as Austria enjoyed 63 percent of possession and forced 13 corners.
Austria last played at the World Cup finals in 1998 while Moldova, bottom of the group with one point, have never qualified.
(Writing by Brian Homewood, editing by Pritha Sarkar)
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