The victory in the driving rain at the Helong Sports Centre, where huge puddles prevented the ball from moving across the pitch, eased the pressure on China's underfire Spanish coach Jose Antonio Camacho.
Two teams qualify from each of the five pools for the finals in Australia and China, Iraq and Saudi Arabia all have three points in Group C, with Indonesia hosting the Saudis in Jakarta on Saturday.
"It was such a difficult game, with such pouring rain. The best part was our players' never-give-up spirit. We deserved the win," the former Real Madrid and Spain coach said.
"Now we have a better chance to qualify. We need to control the game better, to create more goal scoring opportunities."
China started brightly in Changsha but the game turned heavily in their favour just before half-time when Australian referee Ben Williams sent off defender Ali Adnan Kadhim for encroaching at a free-kick.
Sun Ke blasted the initial free-kick over the crossbar but Williams ordered it to be retaken and booked Saif Salman for not being back the full 10 yards. After much jostling in the wall, Kadhim then was guilty of the same offence as Sun attempted to take the kick again and the Australian official awarded the Iraqi a second yellow and then red.
The dismissal forced the 2007 Asian Cup winners to retreat and China dominated the rest of the match but struggled to breakdown a stubborn defensive effort from the visitors until Yu struck from close range in the 92nd minute.
Hong Kong did not leave it as late in their Group E clash with Vietnam, captain Chan Wai Ho heading home the only goal in the 87th minute to leave the 159th FIFA-ranked side dreaming of a first finals appearance since 1968.
"I am really happy to see we played as a team. We did not always use our skill, but our strong mentality," Hong Kong coach Kim Pan-gon said.
"We are in a good position in the group and we should try to make new history for Hong Kong football. We have seven months until our next game, and if we prepare well again, we can make another surprise."
Hong Kong have four points after two games, two less than the United Arab Emirates who came from behind to beat Uzbekistan 2-1 in Abu Dhabi.
The Uzbeks led from the 16th minute when Shohruh Gadoev drilled home a left-footed shot after the home side failed to clear the ball from their penalty area.
But the UAE fought back and Ahmed Khalil and Ali Mabkhout scored a minute either side of the hour mark after taking advantage of the Uzbeks flat backline to steal through for goals.
In Group D, Malaysia also fought back from a goal down at home to beat Yemen 2-1 and join Bahrain and Qatar on three points in the group with the two West Asian sides meeting later on Friday in Riffa.
Also playing later on Friday are Lebanon, who take on Thailand in Group B, their first competitive match since 24 players were hit with penalties for their part in a huge match-fixing scandal involving domestic and international matches.