Smith is Latics' cup hero
Substitute Smith (pictured), who scored twice in the win against Liverpool, came off the bench to produce another piece of magic.
Latics had taken the lead through Jordan Obita, but Everton hit back through goals from Victor Anichebe and Phil Jagielka to take a 2-1 lead.
Then with the four minutes of injury time completed, Smith came to the rescue with a headed goal from Jonathan Grounds' inswinging corner to leave Everton stunned.
And Belgium international Mirallas quickly made an impact providing the assist for the goal which gave Everton a 2-1 lead in the 48th minute.
Mirallas’s corner was met by Jagielka who beat both Lee Barnard and keeper Dean Bouzanis on the six-yard line before heading into the empty net.
Bouzanis prevented Latics falling further behind when he made a good stop low to his left to keep out a goalbound shot from Steven Pienaar.
There was another let off for Latics just short of the hour when Leon Osman just failed to connect with a Mirallas corner from virtually on the goalline.
Latics made their first substitution in the 61st minute when Matt Smith, the two-goal hero against Liverpool, replaced Chris Iwelumo.
And that was soon followed by the introduction of Dean Furman for James Wesolowski.
Latics made their last change in the 77th minute when Robbie Simpson replaced Obita who moments earlier had gone down with cramp.
Substitutes Simpson and Smith linked superby with 10 minutes left when Smith’s shot brought a brilliant save from Toffees’ keeper Tim Howard.
Latics produced a grandstand finish in which Everton were left clinging on for their victory.
Lee Barnard's shot was deflected for a corner.
Simpson then eluded the Everton offside trap and burst clean through only for Howard ti pull off a brilliant save.
Simpson, following up, shot into the side netting under pressure from a tight angle.
And Latics were rewarded at the death as Smith headed home Grounds' corner from inside the crowded six-yard box.
There was only just time to kick off again before referee Phil Dowd sounded the final whistle as the Latics' fans celebrated.
Full-time: Latics 2, Everton 2.