Milner hopeful fired home in the 63rd minute after Wigan's Gary Caldwell had cancelled out an own goal from James McCarthy before half-time.
The win lifts Martin O'Neill's men to within three points of fourth-placed Tottenham, with a game in hand, in the Premier League table.
Remarkably, the victory was O'Neill's first in the league in the month of March since he took charge at Villa in 2006.
Yet Wigan, desperate for points at the opposite end of the table, fully played their part in an absording contest that could quite easily have swung the other way.
Latics are clearly benefiting from the decision to relay their much-criticised pitch and there was some enterprising football on show from both sides.
The visitors responded to their lacklustre draw against Stoke by recalling top scorer Gabriel Agbonlahor, who was troubled by a virus last week, at the expense of former Wigan forward Emile Heskey.
Martinez chose to keep faith with Caldwell after a personal horror show from the defender at the Reebok Stadium and his decision was almost rewarded.
The pace was electric from the start and Wigan created the first openings as Hugo Rodallega fired well wide and Maynor Figueroa sent a fierce drive narrowly over.
Villa were initially slow to get into their stride but they burst into life after 11 minutes as Agbonlahor clipped the ball home from a John Carew flick-on only to see the offside flag raised.
The visitors were denied by the assistant referee again two minutes later as Ashley Young turned in an Agbonlahor cross but replays suggested both decisions were correct, but only just.
Figueroa then tested Brad Friedel with another long-range strike before Carew tried his luck for Villa with an effort that flashed wide.
Agbonlahor found space again only to be denied by a good block from Figueroa and Stewart Downing had an inswinging free-kick from the right tipped over by Chris Kirkland.
Villa took the lead in fortuitous circumstances on 25 minutes after Carew sent a looping header across the box following a Downing cross.
McCarthy was under little pressure as the ball fell his way but he mistimed his clearance horribly and sliced the ball beyond Kirkland.
But Wigan produced the perfect response and levelled within two minutes as Charles N'Zogbia's free-kick was met by a glancing header from Caldwell that took it beyond Friedel.
Both sides remained intent on attack and Rodallega and Young both spurned good opportunities to put their sides ahead.
Carew also went close twice more before the break, first with a cheeky backheel that went wide and then when Kirkland spread himself to save a powerful shot from close range.
The second period began at the same lung-bursting pace with Wigan's Marcelo Moreno curling a shot narrowly wide.
Villa went close again as Stephen Warnock whipped in a dangerous cross but Young's header just missed the target.
Rodallega lined up another shot but Villa defender Richard Dunne showed determination to block.
Villa reclaimed the lead just after the hour as Kirkland flapped at a cross and the ball was only half-cleared as far as Milner on the edge of the box.
The midfielder fired the ball straight back at goal and it somehow found its way through a crowded penalty area to hit the net.
Wigan, having introduced the pace of teenager Victor Moses, tried to respond again but the former Crystal Palace star was crowded out after a strong run.
Rodallega, who felt he was denied a penalty at Bolton, claimed he was impeded in the box by Carlos Cuellar with 15 minutes remaining but referee Steve Bennett saw nothing untoward.
Villa decided to rest Agbonlahor with nine minutes remaining and Heskey entered the fray to generous applause from the home fans.
Wigan pressed on to the end with Moses again showing his pace but he was
unable to carve out an opening.
Latics appealed for another spot-kick for handball against Young but again it fell on deaf ears.
Villa had the last word of the night as substitute Steve Sidwell forced Kirkland to save from distance.
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