With time running out and staring League Two football in the face next season, defender Nelson struck in the first min of injury time to earn his side a vital point.
It was a cruel blow for Brentford who started the game knowing they needed a win to keep up their chances of securing an automatic promotion spot.
But they were left to rue missing a host of chances as they had to settle for a share of the spoils.
Hartlepool keeper Dimitrios Konstantopoulos denied Marcus Gayle on ten minutes with a smart block before midfielder Jay Tabb created another opening.
The Irishman's neat run down the left on 19 minutes ended with a pass to Calum Willock who shot over the bar from eight yards out.
The home side continued to press and Konstantopoulos was again on hand on 31 minutes to block Willock's half-volley from close range following Paul Brooker's corner.
But it was the visitors who blew the best chance of the first half after a defensive mix-up in the Brentford back four.
Keeper Stuart Nelson and Sam Sodje both went for the ball which then fell kindly to Joel Porter who somehow missed an open goal just eight yards out.
Brentford continued to search for the opening gaol after the interval but came up against a stubborn Hartlepool defence. Defender Michael Turner wasted a good chance 11 minutes from time before his team-mate Kevin O'Connor finally made a breakthrough four minutes later.
Brentford won a free-kick on the edge of the Hartlepool area and O'Connor curved in a superb right footer into the top corner of the net.
But just as the home side were celebrating a crucial three points, Hartlepool won a corner deep into injury time which proved costly for the home side.
Thomas Butler's centre fell kindly to Nelson ten yards out and he made no mistake with a half-volley that earned his side a point.