The midfielder was taken to hospital after Brentford defender James Wilson sent him crashing into the advertising boards only 60 seconds after he had come on for Gregor Robertson.
The incident enraged the home supporters as Wilson escaped with a yellow card but, although it fired up Chesterfield, they could not find a reply to Marcus Bean's first goal of the season.
The midfielder headed in a seventh minute corner from Glenn Poole and Brentford would have sealed the points by half-time with better finishing.
Chesterfield were dreadful in the opening 20 minutes but improved and the game turned after Lowry was taken away on a stretcher.
Brentford were forced to defend in numbers for the first time in the match, but with new signing John Halls in excellent form on his debut, they deservedly held on for the victory.
In the end, it was harder work than they might have expected after a first half in which Nathan Elder wasted a clear-cut opening and strike partner Charlie MacDonald headed against the crossbar.
The fans took out their frustration on manager Lee Richardson, but at least his side responded with a better second-half display which could have earned them a point.
Striker Jack Lester, back in the side after injury, would surely have put away at least one of the two chances he failed to convert with a little more sharpness and Ben Hamer had to be at his most agile to keep out a 35-yard shot from Jamie Winter in the 76th minute.
Chesterfield kept pressing but Brentford showed they have a resilience in their football and that denied the home side a share of the points.