Pools started well and were good value for their lead, which came after 25 minutes when teenage prospect Luke James fired in after Jack Baldwin's shot had been cleared.
The promotion chasers levelled after 39 minutes when goalkeeper Scott Flinders, the club's player of the year, made a diving save to keep out Jonathan Douglas' header and Marcello Trotta turned to fire home a low shot.
The Bees did not create much in a flat second period, with their best chance coming in the 87th minute when substitute Tom Adeyemi broke into the area but Peter Hartley blocked his shot.
Hughes said: "In the last 15 minutes of the first half it was Brentford who got a hold in the game and in the second half it was backs to the wall.
"We had three young kids out there playing against a team who are going for automatic promotion, which will do them the world of good.
"In terms of effort it was different class, it's a real tricky playing surface, conditions weren't great for everyone and I wish Brentford all the best in their pursuit of promotion.
"We kept our focus on the game and we need to sit down and won't make any knee-jerk reactions after relegation."