Gillingham 1, Aston Villa 2: Bill Howell's big match verdict
But Villa, who had been on the back foot since their goal, should have doubled their lead five minutes before half-time when Milner crossed for the unmarked Nathan Delfouneso but he volleyed high and wide from eight yards.
The Gills stunned their Premier League opponents by drawing level 12 minutes into the second half.
The goal came when Royce’s long kick was flicked on by Mulligan and Jackson blasted home his 12th goal of the season.
However, rather than galvanising the home side and sparking a famous comeback, the goal brought Villa back to life and they pushed forward.
Delfouneso had the chance to restore the lead when he let fly from 20 yards, but his shot went just wide.
Simon King - impressive at the back for the Gills throughout - blocked a Craig Gardner shot before Zat Knight headed just over.
But Villa were to take the lead again 13 minutes from time.
Young, who endured a frustrating afternoon, broke into the box and went to ground under a challenge from Miller and Stroud pointed to the spot despite the home side’s protests.
After a short delay while a new ball was brought on to the pitch, Milner stepped up and drilled his kick into the bottom left corner.
Gillingham pressed forward in search of another equaliser, but failed to create another meaningful chance, with Young and substitute Marlon Harewood almost extending the lead on the break.
