Junior's priceless goal left Colin Lee a relieved man and Paul Groves totally dejected.
The Brazilian struck two minutes into the second half to guarantee Walsall's survival but end Grimsby's five year stay in Division One.
Lee felt it was his greatest achievement as a manager, and said: "Keeping Walsall up is the same as getting promotion with other clubs. We have worked very hard to get to this position.
"We showed a lot of resilience and mental strength. We got a terrific response and we played well as a unit. We've had four clean sheets on the trot and that's very hard to do.
"The three centre-backs were outstanding. We thought we would come under heavy bombardment at some stage because Grimsby needed to win the game. But we stood up to it well."
Grimsby boss Groves said: "It is a bad day. It is something that hurts. Players' futures are at stake and relegation will bring about financial hardships.
"It's been a long hard road. It's been tough, there is no doubt about that.
"Transfer deadline day was a big turning point for us. We lost John Oster, who gave us a cutting edge. And earlier in the season we lost Steve Kabba who did the same."
Grimsby, desperate for a victory, pushed men forward and went close after eight minutes when full-back John McDermott raided down the right and his cross was met by Michael Boulding whose header went just wide.
Six minutes later Boulding raced on to a Michael Keane through ball but, with the goal gaping, he left the ball behind him and Matt Carbon got back to clear.
Boulding again went close when his header from a Steve Livingstone flick rose just over the bar.
Grimsby keeper Danny Coyne pushed a Jorge Leitao shot around the post.
Boulding figured again, deflecting a Tony Gallimore volley but again the ball flew over the bar.
Junior twice went close for Walsall. First he brought a double save out of Coyne from a tight angle then he lifted the ball over the keeper only for Georges Santos to clear off the line.
Walsall, who forced seven first half corners, again went close when Junior beat three men before setting up substitute Martin O'Connor whose shot was deflected to Coyne.
A comedy of defensive errors led to Walsall grabbing the all-important goal.
Gallimore gave away possession with a poor clearance and when the ball went back in he and centre-back Steve Chettle left it to each other, allowing Leitao to try a shot which was brilliantly saved by Coyne.
Junior pounced on the loose ball to volley home off the underside of the bar.
Grimsby went within inches of equalising in the 73rd minute. Keane's cross from the left was headed over his own keeper by Ian Roper but the ball rebounded off the face of the bar.
Leitao should have made the game safe two minutes later but, racing clear, he saw his lob clear Coyne but drift wide.
Substitute Pedro Matias then saw one effort cleared off the line by Gallimore and when clean through he cleared the bar with his shot.