Second half goals from Tyreke Johnson and Daniel Nlundulu cancelled out Yannick Toure's opener for the visitors as Saints held on to clinch their first crown under the Tunisian at St Mary’s Stadium.
Prior to the playoff, Southampton finished second in the league table behind Wolverhampton Wanderers on goal difference after gathering 43 points from 22 matches.
Jaidi was appointed head coach of the youth team in 2017, five years after he called time on his football career in Southampton.
After the end of the victory that secured his first title as a manager, the former Tunisia captain expressed his delight and also reserved praise for his players' efforts.
"I'm really, really pleased with the boys' performance throughout the season," Jaidi told club website.
"The way they've matured and improved in many aspects, that's what I'm pleased for.
"I said to the boys, we need to finish it off and win something this season. That will stay in our memories and make a legacy for them before either they go into the first-team here, or somewhere else.
"I thank the boys a lot for their trust that they give me and the commitment they put in. The staff sacrificed a lot, and our families.
"The fans who came today and supported us, they didn't let us down. Hopefully that will encourage them to come more and hopefully, we can build on what happened this season for the future."