Spanish defender Miguel Llera struck late on to equalise after the Hyundai A-League side taken the lead after half-time.
In a first half of little chances, Latics looked creative down both flanks and looked comfortable in possession.
A Melbourne corner presented the away side with their first opportunity of the half. The danger was only half cleared and winger James Brown hit an effort over the bar from six yards out.
Latics were difficult to break down and the visitors had to remain patient and keep possession without ever looking to threaten Paul Rachubka in the Latics goal.
Jonson Clarke-Harris had the best two opportunities of the half but failed to test Melbourne City goalkeeper, Tando Velaphi.
Latics trialist Jonathan Forte latched on to an error in the Melbourne back-line and squared the ball to Jonson Clarke-Harris, who was six yards out from goal, but unfortunately the striker scuffed the shot and the defence recovered to clear the ball.
Mike Jones then fed Clarke-Harris, who was in on goal and free of the last Melbourne defender, however he slipped on the wet surface and his shot went well over.
Minutes later, Jones again slipped in a weighted pass to Dayton, who was regularly finding space down the right, but he was tackled before he could feed a teammate.
Latics had threatened down the right and looked to have joy against the visitor's fullback. Brian Wilson’s teasing cross into the box was headed away into the path of the onrushing Mike Jones who tried a speculative volley from distance that went over the bar.
The home side came out unchanged at halftime with Latics looking lively but they fell behind to a well-worked Melbourne goal on 49 minutes. After a slick passing move, the visitors got in behind the Latics defence and Melbourne City half-time substitute David Williams swept home past Paul Rachubka.
Connor Brown played a weighted pass to Jonathan Forte to attack down the left minutes later but his cross was unfortunate not to find substitute Willy Gros and the Melbourne City defence cleared the ball.
Despite substitutes being introduced, Latics struggled to test the Melbourne City goalkeeper, who was given protection by his defenders as efforts were blocked by some committed defending.
A misplaced pass from the Melbourne back-line presented Mike Jones with an opportunity after 82 minutes. Jones bore down on goal, unfortunately his effort was blocked on route to the keeper and saved comfortably.
Latics equalised on 85 minutes after substitute Miguel Llera pounced on a loose ball in the six yard, his effort looped over the stranded goalkeeper and into the back of the net.
The referee signalled the end of the game and the manager would have been happy with his teams display.