Loch, who still leads the overall standings, was fastest in the first run but botched his second -- where he was 26th -- allowing Kindl to win in a combined time of 1 minute, 39.035 seconds.
Germany's Andi Langenhan was fourth, ahead of defending World Cup champion Roman Repilov.
Loch finished 0.36 seconds behind Kindl in 11th place.
With five competitions remaining, five-time World Cup champion Loch leads the overall standings by 571 points, ahead of Kindl on 529.
There was further disappointment for Germany in the team relay, where the doubles pairing of Tobias Wendl and Tobias Arlt was disqualified after a false start. It was the German team's first defeat of the season after three consecutive wins.
Italy's team of Andrea Voetter, Dominik Fischnaller and doubles pair Ivan Nagler and Fabian Malleier claimed the victory in a combined time of 2:43.233, ahead of the United States.