The Gunners looked set to lose for the first time since August in any competition after struggling to fight back following Ivan Cavaleiro's early opener at the Emirates Stadium on Sunday.
But Mkhitaryan came off the bench to snatch a point for Arsenal, his cross from the right wing into the box evading everyone to creep into Rui Patricio's bottom-left corner with four minutes to go.
There was more late drama when Adama Traore was denied by Bernd Leno in stoppage time and Morgan Gibbs-White saw an effort crash back off the crossbar.
Arsenal's third consecutive draw in the Premier League leaves the Gunners three points behind rivals Tottenham in the race for Champions League qualification, while Wolves end a three-game losing streak.
The hosts made a slow start and Cavaleiro silenced the home fans in the 13th minute.
Mesut Ozil's pass was bizarrely dummied by Granit Xhaka, Cavaleiro collected possession in midfield and swapped passes with Raul Jimenez before slotting home a tidy near-post finish.
Wolves could have quickly doubled their lead, but Leno smartly saved from Helder Costa and bravely dived at the feet of Jimenez to prevent the rebound being converted.
Emery introduced Matteo Guendouzi at half-time in search of more tempo and Arsenal improved, Patricio finally called into action to tip away Lucas Torreira's long-range drive.
Hector Bellerin stabbed a good chance over with his weaker left foot in the 70th minute, then the full-back's low cross was turned on to the woodwork by Pierre-Emerick Aubameyang, who had to score.
Arsenal finally found a way through the Wolves rearguard in the 86th minute, a short corner worked to Mkhitaryan, who sent in a cross that curled into the far corner.
Wolves should have won it in stoppage time, but substitute winger Traore was kept out by Leno when he raced through on goal, the Germany goalkeeper then making a sensational fingertip save to tip a 20-yard Gibbs-White strike on to the crossbar.
What does it mean? Title talk premature for Gunners
Arsenal have won only one of their last five matches in all competitions and suggestions they could challenge for the Premier League title now look rather misplaced. Their familiar failings of a lack of leadership and absent-minded defending were on show, though they may well have lost this game last season.
Leno justifies Emery faith
Petr Cech again had to sit on the bench, but Leno made a string of saves to show he deserves to be first choice for Arsenal. The faintest of touches on a late Gibbs-White rocket was a magnificent stop and he also repelled Diogo Jota and Traore in the closing stages.
Award-winner Aubameyang struggles
Aubameyang hit five goals to claim the Premier League's Player of the Month award, but the Gabon striker had little impact and missed a gilt-edged chance before Mkhitaryan struck. Of his five goals in five October appearances, four came from the bench and perhaps he is more suited to being a substitute.
Key Opta Facts
- After winning each of their first six matches against Wolves in the Premier League, Arsenal have only won one of the last three such meetings (D2).
- Since a run of four wins in six matches in the Premier League (D2), Wolves are now winless in each of their last four games in the competition (D1 L3).
- Arsenal have drawn three successive matches at home in all competitions for the first time since August 2012.
- Ivan Cavaleiro’s opener was the first ever time Wolves have taken the lead against Arsenal in a Premier League match, having never been in front at any point in the eight previous meetings in the competition before Sunday's clash.
Arsenal will aim to get back to winning ways at Bournemouth after the international break, while Wolves host Huddersfield Town.