Yoann Barbet fired the hosts in front from a Jota corner before the Spaniard doubled the lead from the spot after Maxime Colin was fouled by Joel Lynch.
Lynch then pulled a goal back by heading past keeper Daniel Bentley.
But Jota restored the Bees' two-goal advantage soon after as he beat two players before firing low into the net.
Lasse Vibe had gone close to opening the scoring early on when he turned his way past Nedum Onuoha before firing the wrong side of the post.
Lynch was then denied by Bentley at the other end before Barbet drilled the ball into the ground and over keeper Alex Smithies to give ninth-placed Brentford the lead.
QPR, who are five points above the bottom three but not yet safe from relegation, were unlucky not to be level at the break with Matt Smith's header being turned away by Bentley and Massimo Luongo hitting the bar from 30 yards in added time.
The visitors thought they had an equaliser when Barbet cleared Conor Washington's effort off the line but the Bees then claimed their second of the afternoon as Jota fired in from the spot after Lynch brought down Colin in the box.
Rangers responded immediately when Lynch headed Luke Freeman's free-kick past Bentley before, just two minutes later, Jota finished his solo-run to claim his 12th goal in 21 games by rolling the ball under Smithies.
Brentford boss Dean Smith: "We know what we are about and we get our heads down and get on with our job. People will always have opinions but all we can do is keep working hard. Results like this mean we can go about our jobs with smiles on our faces.
""It was a comfortable and fully deserved win without us ever really getting near our usual levels. I told them to have clarity about what they do, to have clear heads and no ill-discipline and not to let emotion get involved in the game. They did that.
"We deserved to win but we weren't perhaps as clinical as we have been."
QPR manager Ian Holloway: "We need to think clearly under pressure and we have to get back to doing that every week. We have to dust ourselves down, start again and find a way of playing that's nailed down.
"Brentford played well, I hate to say it, but now it's about how much you care and how you do it. Six games ago we were top of the form table and since then we've had one win to get and we still need it.
"For me it's simple. We have to draw or win next week. We still have work to do. Anyone who is a real QPR fan has to take this one on the chin with dignity because we have to come together to beat Forest."
Match ends, Brentford 3, Queens Park Rangers 1.
Second Half ends, Brentford 3, Queens Park Rangers 1.
Attempt missed. Matt Smith (Queens Park Rangers) header from the centre of the box misses to the left. Assisted by Jake Bidwell with a cross.
Attempt saved. Yeni N'Gbakoto (Queens Park Rangers) header from the centre of the box is saved in the centre of the goal. Assisted by Luke Freeman.
Foul by Nico Yennaris (Brentford).
Luke Freeman (Queens Park Rangers) wins a free kick in the attacking half.
Daniel Bentley (Brentford) wins a free kick in the defensive half.
Foul by Matt Smith (Queens Park Rangers).
Corner,  Queens Park Rangers. Conceded by Josh Clarke.
Attempt missed. Nedum Onuoha (Queens Park Rangers) right footed shot from the right side of the box is too high. Assisted by Joel Lynch following a corner.
Attempt saved. Matt Smith (Queens Park Rangers) header from the centre of the box is saved in the centre of the goal. Assisted by Luke Freeman with a cross.
Corner,  Queens Park Rangers. Conceded by Ryan Woods.
Foul by Nico Yennaris (Brentford).
Massimo Luongo (Queens Park Rangers) wins a free kick in the defensive half.
Justin Shaibu (Brentford) wins a free kick on the right wing.
Foul by Joel Lynch (Queens Park Rangers).
Offside, Queens Park Rangers. Nedum Onuoha tries a through ball, but Joel Lynch is caught offside.
Foul by Nico Yennaris (Brentford).
Yeni N'Gbakoto (Queens Park Rangers) wins a free kick in the defensive half.
Foul by Florian Jozefzoon (Brentford).
Nedum Onuoha (Queens Park Rangers) wins a free kick on the right wing.
Substitution, Brentford. Justin Shaibu replaces Lasse Vibe.
Josh Clarke (Brentford) wins a free kick on the right wing.
Foul by Kazenga Lua Lua (Queens Park Rangers).
Offside, Queens Park Rangers. Yeni N'Gbakoto tries a through ball, but Matt Smith is caught offside.
Offside, Brentford. Romaine Sawyers tries a through ball, but Florian Jozefzoon is caught offside.
Attempt missed. Idrissa Sylla (Queens Park Rangers) right footed shot from the centre of the box is close, but misses to the right. Assisted by Luke Freeman.
Ryan Woods (Brentford) wins a free kick in the defensive half.
Foul by Matt Smith (Queens Park Rangers).
Foul by Jota (Brentford).
Kazenga Lua Lua (Queens Park Rangers) wins a free kick on the left wing.
Corner,  Brentford. Conceded by Luke Freeman.
Attempt saved. Matt Smith (Queens Park Rangers) header from the centre of the box is saved in the top centre of the goal. Assisted by Kazenga Lua Lua with a cross.
Substitution, Brentford. Florian Jozefzoon replaces Sergi Canos.
Substitution, Brentford. Josh Clarke replaces Maxime Colin.
Corner,  Brentford. Conceded by Alex Smithies.
Attempt saved. Lasse Vibe (Brentford) right footed shot from the right side of the box is saved in the bottom left corner.
Foul by Sergi Canos (Brentford).
James Perch (Queens Park Rangers) wins a free kick in the defensive half.
Attempt saved. Jake Bidwell (Queens Park Rangers) header from the centre of the box is saved in the centre of the goal. Assisted by Luke Freeman with a cross.
Two goals in four second-half minutes from midfielder Jota helped Brentford see off struggling London rivals QPR in an entertaining game at Griffin Park.