James Milner's well-taken 13th-minute strike gave Aston Villa a scarcely-deserved 1-0 half-time lead.
But 15 minutes into the second half the Coca-Cola League Two side were level when former Nene Park favourite Jackson raced through the Premier Le
ague side's defence to collect a Gary Mulligan header and fire an unstoppable right-foot shot past Brad Friedel.
However, Milner then fired home from the penalty spot after Ashley Young went down easily following a collision with Adam Miller.
Milner had linked up well with Stiliyan Petrov to net his first goal on his 23rd birthday and although Nathan Delfouneso had a great chance to double the lead, it was Gillingham who had the better of the play in the first half.
The lively Dennis Oli and Jackson were at the forefront of the Gills' attacking play, Oli shooting into the side netting and Jackson heading wide, while Oli could also have won a penalty when fouled by Nigel Reo-Coker right on the edge of the box.
Villa boss Martin O'Neill left out England midfielder Gareth Barry, defender Luke Young and striker Gabriel Agbonlahor, with none of the trio even on the bench.
Nicky Shorey, Craig Gardner and teenage striker Nathan Delfouneso started in their places.
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