With Bryan Mbeumo starting his lengthy spell on the sidelines, Keane Lewis-Potter was rewarded with a starting berth for the Bees, while Wilder kept faith with the same XI from Sheffield United's midweek loss to Liverpool.
Both goalkeepers were mere spectators in the earliest exchanges, although Brentford - who were boosted by the return of Christian Norgaard from a ban - enjoyed the lion's share of possession at Bramall Lane, albeit without any end product to show for it.
The hosts felt hard done by in their defeat to Liverpool regarding officiating decisions, and Wilder's contempt for VAR would not have lessened just after the half-hour mark, as Brentford midfielder Frank Onyeka went in late on Vinicius Souza's upper ankle but got away with just a yellow.
VAR official Robert Jones opted against sending Stuart Attwell to the screen, much to the bemusement of the Blades, and the fortunate Onyeka would have the first shot on target in the 36th minute; his speculative strike was meat and drink for Wes Foderingham, though.
Just one moment later, Sheffield United made inroads behind the Brentford backline, and that move ended with William Osula hammering the ball into the side netting, but Wilder would not have to wait too much longer for the first goal of his second tenure.
In the first minute of injury time, McAtee received the ball from Gustavo Hamer just inside the box, cut inside onto his left foot and curled in a delightful dipping strike into the far side of the net for his first Premier League goal.
Brentford were fortunate not to be 2-0 down 11 minutes after the restart, though, as Cameron Archer squared for Anis Slimane to seemingly tap home from close range, but Flekken crucially denied the Blades man.
Wilder's men looked the more likely to find the back of the net again as the clock ticked down, with Archer and Slimane both coming close in the 80th and 82nd minute respectively, although Yoane Wissa also squandered a good opening for the visitors just one moment before Flekken denied Archer.
The former Aston Villa attacker remained a particular threat in the closing stages and let fly again in the 85th minute, but his curling strike - which left Flekken rooted to the spot - sailed wide of the Bees goal.
Surviving one last penalty shout as Norgaard went down in the box, Sheffield United drew themselves level on points with 19th-placed Burnley are are now just two points adrift of safety, while the Bees - who were left incensed as their spot-kick appeals fell on deaf ears - remain 11th.
Sheffield United now have an intimidating trip to Chelsea up next on December 16, while Brentford host high-flying Aston Villa next Sunday.No Data Analysis info