Hugo and Baiano, two of UAE champions Al-Wahda's three Brazilians, scored in the last five minutes of the first half to virtually put the match beyond Hekari, a team founded in Papua New Guinea only seven years ago.
Fears that the home team might fail to progress from the opening match as Al-Ahli did last year when they lost to Auckland City, disappointing the organisers and FIFA, were dispelled after a nervous opening half hour.
"The pressure on the team was great, I could feel it from outside, some of our players couldn't cope with it," Al-Wahda's Austrian coach Josef Hickersberger told the post-match news conference.
"Hekari United started well with long balls and they are good in the air. We started to play the same way, which is not our style," he added.
"Fortunately, we have experienced players. The Brazilians turned the match around with help from our UAE internationals."
Hekari's coach Tommy Mana, who is from the Solomon Islands like several of his players, said: "For any team to beat Al-Wahda they will have to work very hard."
Al-Wahda face Asian champions Seongnam of South Korea in their quarter-final on Saturday. Concacaf champions Pachuca of Mexico meet Africa's TP Mazembe of DR Congo in the first quarter-final on Friday.
Brazil's Internacional, the South American champions, and Europe's Inter Milan have byes into the semi-finals.
