However, having failed to convert his opportunities earlier on, Deeney made amends in the 50th minute when he turned inside the penalty area, before firing a low shot beyond the reach of Rob Green.
The visiting Hornets continued to push forward in search of a second goal, but Green and his defence held firm.
Then, their stubbornness was rewarded 14 minutes from time when midfielder Joey Barton wrong footed Almunia with a curling effort from 20 yards out.
Having been pegged back, Watford responded positively, but when Deeney was presented with an opening, he shot inches wide of the upright.
That miss would prove to be a costly one in the 90th minute as Austin curled in the winning goal, which has secured QPR's place in the playoffs.