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.
BRAZILIAN BRACE
Some rudimentary defending from both sides, particularly Hekari, made for some thrills at both ends, but Al-Wahda made better use of their possession with Brazilian holding midfielder Magrao a commanding figure in the middle of the park.
Al-Wahda went ahead when a high cross from the right fell to Mahmood al-Hammadi on the left of the box. He brought the ball down for fellow midfielder Hugo to unleash a low, left-footed shot from the edge that went inside the far past.
Four minutes later, Baiano ran onto a fine through ball from al-Hammadi into the box on the right and beat keeper Simione Tamanisau with a low shot inside the near post.
Substitute Adulraheem Jumaa headed the third 19 minutes from time from a cross from the left which left-back Koriak Upiaga and Tamanisau failed to clear.
A 23,800 crowd in the 42,000-capacity Mohammed bin Zayed stadium will have fallen short of UAE expectations as they attempt to persuade FIFA to bring the tournament back to Abu Dhabi in 2013 after it returns to Japan for the next two years.
Victory for Al-Wahda, however, should boost the numbers in their next match.
