Both sides created numerous chances as they chased points for contrasting reasons but the quality of 24-year-old Milner, who claimed his 10th goal of the season, proved the difference.
The decisive strike at the DW Stadium came just after the hour, Milner firing home through a crowded penalty area after the Wigan defence had struggled to clear a corner.
Villa had led in the 25th minute after a bizarre own goal by James McCarthy - the Republic of Ireland international somehow sliced a clearance into his own net - but Wigan equalised immediately with a Gary Caldwell header.
Villa boss Martin O'Neill was in no doubt where most of the credit for victory was due, hailing the efforts of Milner.
"It was an extraordinary performance by a really good player," O'Neill said.
"Since he has stepped into central midfield his game his improved tenfold and he continues to go from strength to strength.
"When you play wide you depend on other people giving you the ball to get into the game but when you have got that determination and energy, you might as well use it in the centre of the field.
"It is something we have been crying out for, a midfielder scoring double figures, and he has been sensational."
Villa remain seventh but victory moved them within three points of fourth-placed Tottenham with a game in hand.
O'Neill added: "It was important for us to close the gap. We did that tonight and it was a brilliant win for us."
Villa also had two goals disallowed and Wigan's Chris Kirkland was the busier of the two goalkeepers but the hosts showed plenty of attacking intent themselves.
Hugo Rodallega and Maynor Figueroa where their chief threats while Caldwell's performance was a personal triumph after a horror show in Saturday's 4-0 thrashing at Bolton.
Nevertheless, defeat leaves Roberto Martinez's men just four points above the relegation zone ahead of a crunch clash with fellow strugglers Burnley at the weekend.
Martinez said: "It was a really even game, really open.
"Both sides were probably tired after Saturday but they gave everything.
"I couldn't see much between the two sides. I am just disappointed about the own goal and a soft goal from a corner after a poor clearance.
"That leaves a bad taste because I don't think the players deserved to get nothing out of the game.
"I felt the players shared everything in that game and it should have been a draw."