Boston Town bowed out of the FA Vase as this tie finally took place a week later than originally planned.
Midland League visitors Atherstone got off to a fast start, with goals from Lewis Collins and Ryan Quinn giving them a 2-0 lead inside the first 20 minutes.
In his first game as Boston Town manager, Chris Funnell was hampered by the absence of two key players – the in-form Harry Limb, who had scored six goals in his previous two games, and defensive rock Richard Ford.
The returning Fraser Bayliss gave the Poachers hope when he pulled one back after 58 minutes.
But Atherstone killed the tie when Ryan Harkin made it 3-1 with 10 minutes left.
Town: Portas, Tate, Millar (Doran), Burdass (Beeson), Worthington, Wilson, Dakin (Bad), Adams, Nuttell, Maddison, Bayliss; unused sub: Borbely
Boston Town FC 