A solitary strike for the hosts was enough to see them edge past Jurgen Klinsmann's side on Tuesday night
Marcel Koller's men narrowly missed out on qualification for the World Cup after they finished third in Group C of the European section.
But the hosts went a little way to putting that disappointment behind them in Vienna, edging to a slender friendly victory in a game of few chances.
Jurgen Klinsmann's USA - who will be making their seventh straight appearance at the World Cup next year - dictated much of the encounter, but it was Janko's close-range strike after 33 minutes that proved the difference between the two sides.
The visitors had the better of the opening exchanges, with Jozy Altidore and Aron Johannson both going close, before Geoff Cameron's header appeared to strike the hand of forward Marko Arnautovic before being clawed off the line by goalkeeper Robert Almer.
The Americans claimed that the ball had crossed the line, but the referee failed to award either a goal or handball.
And Klinsmann's men were made to pay for their missed opportunities as Austria scored with their first real chance of the game, as Janko emphatically converted from Gyorgy Garics right-wing cross.
Altidore turned Mark Bradley's corner narrowly wide just before the interval, but the United States almost fell further behind three minutes after the break, as Martin Harnik missed the target with a superb curling effort.
Despite that scare, Klinsmann's side continued to push for a leveller, although they struggled to create too many clear cut chances as Austria produced a determined defensive display.
Substitute Terrence Boyd went closest to netting the equaliser on 71 minutes when the 22-year-old Rapid Vienna striker fired just over the crossbar following a smart turn.
That proved to be the visitors last real opportunity as they ended 2013 with just their second defeat in their last 18 games.