Charlie MacDonald looked to have given the hosts all three points after opening the scoring with only 17 minutes left, but Humphrey slammed home just three minutes after entering the fray.
In truth, neither side deserved to win after what was a disappointing game, but it will be Paul Simpson's visitors who will be the happier after salvaging a draw when it seemed beyond them.
But the first half in particular was a dire affair. These teams should have been high on confidence, with Brentford unbeaten in 11 and Shrewsbury having scored 25 goals in their dozen games, but there was no sign of an end product from either side.
The only moment of real interest came on the half-hour as tensions threatened to boil over. A tough challenge on Marcus Bean ended with players from both sides piling in, with Brentford captain Adam Newton and Shrewsbury left-back Marc Tierney at each others throats before calm was restored.
The break in play appeared to galvanise Shrewsbury rather than their hosts, with Grant Holt hitting the side-netting.
Andy Scott's Brentford may be second in the league, but only four players had found the back of the net so far this season - and it was hard to see any sign of where a goal was coming from.
Yet just as it appeared both sides had settled for a point the home side made the breakthrough.
Marvin Williams was the instigator, battling through two challenges on the right-hand side of the area before feeding MacDonald, who showed a superb poacher's instinct to swivel on the ball before firing home into the far corner with his left foot.
It was MacDonald's sixth league goal since his summer move from Southend United, and it was well deserved as he was one of the few players on the pitch to show any sign of true invention or creativity.
But Simpson made an inspired substitution that paid immediate dividends for his side.
Humphrey had only been on the pitch for three minutes when a long free-kick broke to him on the edge of the Brentford box. The winger took one touch to get the ball out of his feet before lashing beyond goalkeeper Ben Hamer for his first goal of the season.