Brazilian striker Jo steered Manchester City towards the group stages of the UEFA Cup with his first goals for the club.
The 21-year-old, a £19million summer signing for CSKA Moscow, helped turned the first round first leg match in Cyprus on its head.
He scored in the 59th and 72nd minutes after Klodian Duro had made the breakthrough for Omonia.
City were rocked after outplaying their opponents in the first half but then launched a spirited fightback.
They will now approach the second leg in a fortnight with confidence, although the margin of victory could have been greater with Jo, in particular, wasteful before his two goals.
Hughes was looking for his side to get a quick foothold in the tie after they struggled to beat the Danes of FC Midtjylland in the last round.
City almost made the breakthrough in the second minute when Robinho found space in the penalty area.
The £32.5million buy from Real Madrid rattled in a shot that goalkeeper Antonis Giorgallides did well to parry to safety.
City kept up the pressure and Stephen Ireland saw his effort go over the crossbar after Robinho and Pablo Zabaleta had linked up.
Omonia were again forced on the back foot in the 15th minute and Wright-Phillips' shot from the edge of the area was turned around the post by the goalkeeper.
City squandered a glorious chance of taking the lead in the 27th minute when Ireland squared the ball across the face of the area and into the path of Jo.
However, with the goal gaping, the Brazilian appeared to take his eye off the ball and he sliced his effort wide.
There were groans from the 900 City fans, who were packed into a corner of the ground at such an astonishing miss.
Elano then skipped forward in the 39th minute only for Hamad Ndikumana to block his effort.
A minute later Jo came within inches of giving City the lead when his shot beat the goalkeeper but came back off the post.
It was Ireland's turn to curse his luck in the 43rd minute after being set up by Jo, his effort also coming back off the woodwork.
But City were stunned in the 49th minute when Omonia opened the scoring.
Albania midfielder Klodian Duro sent the home fans into a frenzy with a stunning free-kick from 18 yards that whistled past Joe Hart.
City roared back and Ireland's goal-bound shot was booted clear by Giorgallides.
Then Jo was again wasteful in the 55th minute after a one-on-one with the goalkeeper, his shot coming back off the crossbar.
City drew level four minutes later after cutting the Omonia defence apart with a swift counter-attack.
Wright-Phillips raced to the byline and released Jo, who made no mistake with his first goal for the club following his £19million move from CSKA Moscow.
That stunned the crowd and it was no more than City deserved given the amount of possession they had enjoyed with no reward.
City then went ahead in the 72nd minute thanks to Jo's second goal to put them firmly in the driving seat.
The big striker made no mistake from close range after getting on the end of a cross from Zabaleta.
Then Micah Richards strode into the area with a minute of the game remaining but failed to test the goalkeeper as City saw out the game and got the victory they craved.