Having pulled off a 4-1 home victory in the first leg three weeks ago, the Lebanese entered the return leg strongly fancied against hosts India, who had a mountain to climb, needing to win by at least three clear goals to advance.
The all-important match, originally scheduled to be staged in Chennai on Sunday, was forced to be relocated to Goa on Tuesday due to torrential rain, something which made life difficult for both sides.
While the visiting side looked happy to sit on their three-goal advantage, India went on the attack and they opened scoring through Sunil Chetri on the half hour. However, after the interval, Lebanon substitute Mohamad Ghaddar scored to leave India's hopes hanging by a thread.
Cheered on by the home crowd, the hosts threw everything forward but their woes increased when Ghaddar scored again three minutes from time, leaving captain Baichung Bhutia's last-minute equaliser nothing more than a consolation.
Thanks to the victory, Lebanon join the other ten highest ranked Round 1 winners and the 'big five' of Australia, Iran, Korea Republic, Japan and Saudi Arabia who receive a bye, into the third stage of the competition, which features 20 teams.
The eight lowest ranked Round 1 winners have been paired and will play each other on a home and away basis on 9 and 18 November to complete the 20 team line-up for Round 3.
Meanwhile, Singapore were awarded by FIFA a 3-0 victory against Palestine, who failed to be present for the second leg of their time. The result, coupled with their 4-0 away win in the first leg, saw Singapore through to complete the ties for the second round of Asian qualification.
2010 FIFA World Cup South Africa
Asian Qualification Round 2
*The two-legged ties will be played on Friday 9 and Sunday 18 November.