The Brazilian striker's contribution in the second half was vital as Klodian Duro had given the home side a shock lead in this first-round first-leg match.
Jo, a £19million summer signing from CSKA Moscow, responded with clinical finishes in the 59th and 72nd minutes.
He grabbed the equaliser by escaping his marker and taking advantage of Shaun Wright-Phillips' cross.
Jo grew in confidence and added to his tally after being set up by Argentinian full-back Pablo Zabaleta.
It was the 21-year-old's reward for keeping his head after a glaring miss in front of the posts.
With Robinho and Elano also in the starting line-up Hughes went for an attacking formation and it paid dividends in front of a partisan crowd.
Hughes said: "Jo was a little bit deliberate for the first opportunity. He tried to make sure of scoring.
"The pitch was a little bit slow and bobbly but he worked really hard for the team and I am delighted he got his reward.
"They were two good finishes and he will settle down now. When a new player, especially a striker, comes to a club it is important to get off the mark and make an impression and he did that."
Hughes was pleased with the way his side refused to panic after Duro had opened the scoring with a stunning free-kick in the 49th minute.
"We had a lot of possession up until then and sometimes you feel it might not be your night," said the City boss.
"But I saw good signs and good qualities. We did not panic and played the right way. We created more opportunities and won quite comfortably."
Hughes, however, is refusing to take the second leg for granted.
He said: "Omonia worked extremely hard and are a decent side. We knew we had to play well and there is still work to be done in the return match.
"However we are in a strong position, especially as we have away goals on the board.
"I thought we gave a professional performance in Europe and got the job done in the end."