Watkins grabbed his 20th of the season to add to goals from Julian Jeanvier and Bryan Mbeumo to finally end the dogged resistance of a Boro side who levelled twice through Lewis Wing and Ashley Fletcher.
Brentford took the lead midway through the first half, centre back Jeanvier bundling home his first of the season in a goalmouth melee.
The Teesiders hit back just before the hour when Wing picked up a loose ball on the edge of the box and smashed a low drive just inside the left upright.
But Boro reacted well and were level again three minutes later when Fletcher nipped in between a static Bees defence to head home Marcus Tavernier's corner.
The visitors looked set to deny Brentford their first ever double over them until Watkins popped up in the box to coolly sidefoot home Christian Norgaard's driven low cross to clinch the points.
Benrahma went close again minutes later but his blistering volley was deflected over the bar by a desperate lunge from Boro defender Jonny Howson.
The Bees took the lead when Mathias Jensen's deep corner was headed back across goal for Jeanvier to react quickest in a sea of legs to get the decisive touch.
Boro should have got a foothold back in the game just after the half hour when good work from Marvin Johnson down the left found Tavernier but his first time shot was saved low at the second attempt by Raya.
After the break the game opened up and Boro pressed forward, Johnson slinging in a cross from deep that sailed over Raya only to bounce back off the far post.
At the other end Dasilva forced a smart save from Pears before Wing did likewise at the other end with a dipping volley from 25 yards.
He was given time to test the stopper but the Bees defence didn't learn and he was allowed to fire home the equaliser minutes later.
The flurry of goals took it to 2-2 before Brentford started to exert more control and Emiliano Marcondes went close with a cheeky free kick that almost caught out Pears at his far post.
Fletcher might have nicked the points with 10 minutes to go but he failed to get enough on Britt Assombalonga's cross and the ball sailed high and wide.
Benrhama twice squandered decent efforts as the clock ticked down, once firing over from a central position after a slick six-man move that ended with a low Rico Henry cross.
In the end it was Watkins who had the final say and sent Boro back to the north east empty handed.