The Bucks lost 4-0 on aggregate against Barrow in the play-off semi-final in 2008, then last year they slipped to a 1-0 defeat at Gateshead in the final.
Smith had said he felt he was the right man to put things right and had hoped the board of directors would renew his contract.
Captain Stuart Whitehead will take charge of the Bucks against Vauxhall Motors on the final day.
You can follow the latest news of the departure of Rob Smith on BBC Radio Shropshire 96 FM.
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