Austria, who missed out on the World Cup, won with a freak goal by Louis Schaub in the 87th minute as their new coach Franco Foda got off to a winning start.
Schaub took a free kick near the touchline around 35 metres from goal and the ball floated over a pack of players and into the net without anyone getting a touch.
Austria had gone in front after five minutes with a Marcel Sabitzer goal but Uruguay took control after Edinson Cavani headed the equaliser in the 10th minute, his 40th goal for his country.
The South Americans squandered a flurry of chances with Giorgian de Arrascaeta thumping the ball against the post and Cavani firing over when he had a free shot on goal.
Forward Luis Suarez was rested by Uruguay to help his recovery from a knee injury.
Uruguay have played four friendlies in Europe this year, producing three defeats and a draw against Poland.
(Writing by Brian Homewood in Berne; Editing by Toby Davis)
