Grimsby manager Paul Groves tried to put a brave face on things after relegation to Division Two after five seasons at the higher level.
But he admitted it was a black season for the club and there were futures at stake for several players who had given long service.
Grimsby at least went down with a fight but two missed first-half chances from Mick Boulding proved decisive.
Walsall, with five men at the back, were strong and resilient and once they had got their noses in front they were in no mood to give anything away.
Victory for the Saddlers meant they had stayed at this level for three seasons for the first time in their history. The goal when it came was a soft one from Grimsby's point of view.
The Mariners gave the ball away in midfield and though keeper Danny Coyne saved well from Jorge Leitao he could do nothing about Junior's follow-up shot in the 45th minute.
Grimsby pressed for the rest of the game and the closest they came to an equaliser was when central defender Ian Roper headed against his own bar.
Grimsby’s only shot on target of their own making came two minutes from time but midfielder Michael Keane's effort was easily saved.
Despite being relegated with two games left Groves said they were important matches and then it was a case of taking stock in the summer.
Walsall boss Colin Lee, after saluting his players’ efforts, said there would be a different financial structure next season when he would be looking to consolidate the club’s status in division one.
But he was just delighted the Saddlers would be there again next season and safety had been accomplished with two games left.