Jota inspired Brentford to their first double over QPR since 1965 as his brace downed Ian Holloway's side.
The Bees were the better footballing side throughout and, only when the visitors tried to get physical did they get close to Dean Smith's side.
Brentford took the lead midway through the first half as Jota's corner was volleyed home by Yoann Barbet for his first league goal of the season.
The Bees had a stroke of luck when Conor Washington's header appeared to cross the line with Yoann Barbet seeming to head it into the roof of the net but referee James Adcock and his assistants saw it otherwise.
Moments later, Joel Lynch had fouled Maxime Colin in the box and Jota sent Alex Smithies the wrong way before the defender pulled a goal back when he headed home from a free kick two minutes later.
Just 120 seconds later, the Spaniard scored the goal of the game and arguable Brentford's goal of the season when he picked up Nico Yennaris' cross-field ball, left Jake Bidwell for dead and slid the ball home to ensure a two goal cushion.
After seven minutes added on, where QPR attempted to mount a fightback, the Bees claimed all three points to leave their rivals looking over their shoulder at the relegation zone.