Chris Turner's Wednesday side finished the season odds-on favourites for a quick return to the First Division.
The Hillsborough outfit, relegated two weeks ago at Brighton, ended with a run of seven games without defeat and Turner is confident Wednesday will be in the promotion pack in 12 months time.
Lloyd Owusu and Alan Quinn staged the Wednesday fightback after Walsall had taken a 56th minute lead.
Walsall's Spanish full-back Zigor Aranalde almost found a way through in the 18th minute with a stinging cross from the left that was cut out by centre back Leigh Bromby as he guarded the near post.
Wednesday failed to clear seconds later and when Vinny Samways lashed in a low effort which was deflected to Junior, the Brazilian striker scuffed the ball dragging his shot harmlessly wide of the target.
Wednesday midfielder Paul McLaren went close with a shot from the edge of the area which dipped inches over the top and Shefki Kuqi dragged a header wide as the Owls looked for a breakthrough.
But it was Walsall who almost snatched the lead in the 38th minute. Leading scorer Junior linked well with Carl Robinson before curling a 22-yard left-foot shot beyond Kevin Pressman's reach, the ball flying wide of the far post.
The 26-year-old Brazilian showed a touch of class minutes later cheekily slotting the ball between Bromby's legs before finishing with a fierce shot which cannoned against Pressman before Kuqi was foiled by James Walker, the Walsall keeper blocking his close-range header at the near post.
The Finnish international should have snatched the lead for Wednesday on 53 minutes after skipping past his marker but fired wide from 16 yards before Walsall went ahead in the 56th minute, Junior picking out substitute Pedro Matias who beat Pressman with a low shot from 15 yards Substitute Owusu grabbed the equaliser in the 67th minute, two minutes after coming on, Ashley Westwood heading the ball to his feet as he steered a shot past Walker from 12 yards. Alan Quinn hit the winner 14 minutes from time.