But the Bees staged a rousing fightback and Josh Dasilva gave them hope in the 84th minute before fellow substitute Bryan Mbeumo levelled and Ollie Watkins pounced for the winner deep into stoppage time.
It was a scoreline that never looked on the cards as the hosts lacked urgency until the thrilling finale, with Millwall resolute and well organised.
Watkins has now missed three of his last four penalties.
Brentford were dealt another blow just before the break when their only recognised centre forward Nikos Karelis was stretchered off after falling awkwardly.
They stretched their advantage 10 minutes after the break when Wallace finished coolly from the penalty spot after Watkins hauled Hutchinson to the ground from a corner.
It was a sucker punch for Brentford, who dominated possession and created a string of clear-cut chances but lacked any real cutting edge.
That changed in dramatic fashion in the closing stages when Dasilva coolly passed the ball into the far corner of the net from the edge of the box to finally break Bialkowski's stubborn resistance.
They were level four minutes later when Mbeumo chanced his arm with a speculative shot which took a deflection and looped over Bialkowski and into the far corner.
Brentford poured forward sensing a winner and the Millwall defence failed to deal with a Benrahma cross which was recycled and ended at the foot of top-scorer Watkins whose half-volley beat the keeper.
Seconds before the end the game threatened to boil over when Wallace flew in studs-up on David Raya, sparking a 14-man brawl. The striker escaped with a yellow card along with the Bees' Julian Jeanvier.
Brentford moved up to 13th with the win, which leaves Millwalll still winless in their last 10 away league London derbies.