Milner, who is 23 today, gave the Claret and Blue an early lead as he brilliantly bent in a Stiliyan Petrov's cutback from the edge of the area.
He then scored a penalty with just over ten minutes remaining after Ashley Young had been brought down by Gills captain Adam Miller.
The home side had threatened to cause an upset when Simeon Jackson turned Zat Knight and fired past brad Friedel in fine fashion on 57 minutes.
But, Villa gradually gained a foothold in the game and in the end Milner's penalty gave the Premier League side a win, which their second half pressure had merited.
Banana skins are obviously anticipated in the F.A Cup third round and with ITV showing the game it was obvious that Villa's lower league opponents would lift their game.
The Claret and Blue were forced to change the line-up which beat Hull on Tuesday as Gabby Agbonlahor, Gareth Barry and Luke Young missed out through injury.
Virtuoso
And early on, the changes seemed to affect them as Gillingham pressed forward but the hosts failed to create any real chances and Villa made them pay.
A typical counter attack saw Milner curl the ball into the net after playing a neat one two with Petrov.
It was a virtuoso effort from the wideman, who was certainly in the mood to celebrate his birthday in style.
Nathan Delfouneso was then given the chance to put Villa two up but he shot over the bar from a fine Milner cross.
Although Villa had the best chances it was Gillingham who dominated possession throughout the half and they missed a couple of half chances.
After half time they were rewarded for some good football as Knight was turned by Jackson, who finished in style. It was a goal fit to grace any level of football and one which gave the home side real hope of causing an upset.
But, Villa stepped it up and after peppering the home penalty area Young was given the chance to weave his way into the box where he was barged over by Miller.
Cake
It was a clumsy challenge from the captain and Young, as he does so well, made the most of it.
There was confusion as to who would take the penalty with regular taker Barry out, but Milner finally put the icing on his birthday cake with a cool side footed finish.
Gillingham then threw the proverbial kitchen sink at their Premier League opponents but they could not find a way through.
After the game, Villa were handed an away tie against Cheltenham or Doncaster, who are yet to play as their fixture at Whaddon Road was cancelled on Saturday.
The Claret and Blue are just pleased to be through and not facing Manchester United who halted their progress to the fourth round in the last two seasons.
The man who pulled Villa out of the hat was Roberto Di Matteo and fans may just be wondering whether they are set to reach the final again just as they did when Di Matteo scored the winner for Chelsea in the last ever F.A. Cup showpiece at Wembley in 2000.
Milner, though, will just be happy to see Villa through to the next round for now and enjoy what was very much his day.