Hartlepool looked set to end the season with a fifth defeat in six games, before Brown ghosted in to the penalty area in the third minute of stoppage time to convert a David Foley cross.
To add to Walsall's late agony, a section of their supporters then staged an after match demonstration calling for the departure of the club's owner Jeff Bonser following the team's disappointing end to the season when they slipped out of the play-off race.
Mooney had hoped to make it a leaving party to remember as the veteran striker had looked to have ended his career in England in the best possible way after his 12th goal of the season had fired Walsall into a 2-0 lead after just 15 minutes.
Mooney, who is set to join the Spanish side UD Marbella, was making the 759th appearance of his 19-year career and showed he is as sharp as ever in front of goal.
After setting up Walsall's ninth minute opener for Michael Dobson, the well-travelled marksman doubled their advantage in the 15th minute.
Walsall, who had lost their previous three games, were cruising after the quick-fire double, but a Michael Mackay strike after 19 minutes handed Hartlepool a route back into the match.
It was a lifeline that Hartlepool hung on to right until stoppage time when Brown pounced.
Hartlepool had started the game in positive fashion with Foley and Mackay both firing wide from long range.
Walsall were able to overcome that early storm and Dobson handed them the initiative with his first goal of the season.
Richard Taundry picked out Mooney and his neat pass was converted by Dobson from the edge of the area.
Dobson repaid the compliment six minutes later - setting up Mooney whose clinical finish gave Hartlepool goalkeeper Arran Lee-Barrett no chance.
To their credit, Hartlepool refused to buckle after that double setback and were rewarded for their positive response through Mackay's fifth goal of the season.
He reacted fastest at the far post by firing home a cross from Richie Humphreys through a crowded goalmouth.
It was a catalyst that sparked Hartlepool into life and they went on to dominate the second period.
Andy Monkhouse headed weakly at goalkeeper Clayton Ince from close range following am excellent cross from Mackay and Sam Collins saw his header cleared off the line by the well placed Alex Nicholls.
Mackay was then guilty of an awful miss after blazing over the bar from six yards and goalkeeper Ince blocked a point-blank drive from Foley before Brown's strike rescued them.