The hosts had special dispensation from the Football League to wear a camouflage kit – commemorating 100 years since the start of the First World War – but they found themselves 2-0 down after Andre Gray’s double either side of half-time.
Millwall fought back with two goals in two minutes from Lee Gregory and Alan Dunne – his first since March 2013 – just before the hour mark.
But Shittu’s unfortunate own goal handed the Bees victory, their third in a row, and with it a place in the top six.
Brentford made the brighter start with Moses Odubajo’s pace down the right causing the hosts all kinds of problems, but several poor deliveries left Jon Toral and Gray frustrated.
However, Lions forward Gregory was soon calling for a penalty when his shot on goal was blocked by Harlee Dean.
The referee, James Adcock, adjudged it wasn’t with an arm and Lee Martin’s hanging cross hit David Button’s near post straight from the subsequent corner.
Jota had a great chance moments later as Brentford broke from a Millwall corner, but his shot flew well over much to the frustration of his team-mates.
On 20 minutes Gray was put through by Toral but, one-on-one with goalkeeper David Forde, the Brentford striker fired a low shot just past the far post.
Toral was then visibly frustrated not to be awarded a penalty when confusion in the Millwall defence resulted in Shittu’s clumsy challenge on the striker.
Martin had Millwall’s best chance of the half, after Matthew Briggs sent a low cross into the box, yet the former Manchester United winger saw his close-range attempt blocked by Button.
And three minutes before the break Gray’s intelligent runs finally came to fruition when he latched onto an Alex Pritchard through ball and sent a low shot past Forde to give the visitors the lead.
On 56 minutes it was 2-0 when Alan Judge put the ball through for Gray who looked decisive yet again as he sent a shot low into the bottom right corner – the start of a frantic 10 minutes in which four goals were scored.
On 58 minutes Martin sent a looping cross into the box, which Shittu headed in off Gregory, before Millwall captain Dunne equalised just a minute later when he fired the ball into the bottom corner.
Gregory hit the bar just moments later with a powerful header from an accurate Briggs cross, but the impressive Gray turned provider as Brentford grabbed the winner – his low cross diverted into his own net by Shittu on 66 minutes.