Despite dominating ball possession in the first half, Ukraine failed to create a concrete chance to open the scoring.
It was an impressive display from Northern Ireland, who fought their way back into the game after having struggled for the first-half possession - winning just 35% in the first 45 minutes.
The deadlock was broken by Northern Ireland four minutes after the break, with McAuley heading home a brilliant cross from Oliver Norwood to beat goalkeeper Andriy Pyatov.
Both teams struggled in the sodden conditions as a hail storm then battered the pitch and on 58 minutes Czech referee Pavel Kralovec decided to halt the game.
The players were back out three minutes later and Ukraine fought for the equaliser.
Ukraine peppered their opponents’ goal with long-range shots before McGinn slammed in injury time to wrap up a famous win for Northern Ireland.
Germany were held to a goalless draw by Poland in another Group C match later the same day.
Germany are leading Group C with four points, followed by Poland with four and Northern Ireland with three.
Germany will play Northern Ireland and Ukraine face Poland on June 21. A draw will be enough to fire either Germany or Poland towards the knockout stage.
Earlier on June 16, Daniel Sturridge struck deep into stoppage time to hand England a 2-1 win over rivals Wales to move top of Euro 2016 Group B with four points.
