The fairy-tale ending wasn’t to be for the Pilgrims’ York Street ground as Alty made it two promotions in three seasons.
There were only 13 minutes on the clock when Craig Elliott was forced to replace striker Jake Wright with Dominic Knowles due to injury.
Boston went close from a quick corner when Andi Thanoj whipped a dangerous ball into the box that was almost scrambled in at the back post.
Jay Rollins and Jordan Thewlis were getting joy down the Boston wings, but neither could supply the final killer ball to edge the hosts ahead.
Toby Mullarkey fired a warning shot for Altrincham, but his shot deflected high and out for a corner.
Luke Shiels headed narrowly over with seconds left of the first half, but the sides went in level, with no goals, at the interval.
Mullarkey had another chance for Altrincham, surging forward before his tame shot was comfortably gathered.
Altrincham’s best chance so far in the game fell to Jordan Hulme who nodded just wide at the back post from Elliott Durrell’s deep cross.
Peter Crook had a moment to forget just after the hour mark when he looked to have gathered the ball with ease, but it slipped from his grasp and Mooney pounced to give Alty the lead.
Both sides continued to push but chances were at a premium for the remainder of the game, Altrincham hanging on.
Boston United: Crook, Challoner, Whittle, Platt (Nicholson 84’), Garner, Shiels, Thanoj, Abbott, Wright (Knowles 13’), Thewlis (Mulhern 69’), Rollins Subs not used: Ainge, Warren, Willis
Altrincham: Thompson, Richman, Hampson, Mullarkey, Hannigan, Moult, Mooney (Mahon 69’), Lundstram, Hulme (Williams 86’), Hancock, Durrell (Peers 69’) Subs not used: Harrop, Hooper, Wynne