The Shrimpers held their nerve to win 4-2 on penalties after the game had ended in a 0-0 draw.
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Maher was delighted to see his squad celebrate in front of close to 24,000 Blues fans – little more than two years after the club came close to folding amid huge financial issues.
“This is amazing,” said Maher.
“These players have been through so much and they deserve it.
“These players have been amazing and, after the disappointment of last year here in the play-offs it’s nice to put that bed.
“If we can add the right ones then we can be challenging for promotion next year, but this is a special day in itself.”
The Shrimpers were twice denied by the woodwork during the game with Harry Cardwell hitting the post and Keenan Appiah-Forson the crossbar.
But Blues held their nerve to triumph on spot-kicks with Gus Scott-Morriss scoring the decisive effort after Collin Andeng Ndi had saved Wealdstone’s first two penalties.