Roda Antar was the match winner, with the creative midfielder's 28th-minute strike the first goal Lebanon, ranked 124th by FIFA, had scored against their more illustrious opponents in this their eighth meeting.
His team mates then defended bravely and wasted time much to the irritation of Iran, who struggled badly on the atrocious pitch which lacked grass in several areas as the home side claimed the landmark win.
Lebanon, competing in the fourth round of Asian World Cup qualifying for the first time, now have four points from four matches in the five-team pool, level with Iran and Qatar who have played one game fewer.
The result heaped more pressure on Iran coach Carlos Queiroz, the former Real Madrid and Portugal boss who has been criticised for his tactics as the team have struggled for goals.
On Tuesday, they dominated possession and territory but came up against in-form Lebanese goalkeeper Abbas Hassan, who thwarted them on several occasions.
The headband-wearing goalkeeper, who was shown a yellow card for time-wasting, produced a string of solid saves, with his 95th-minute stop of Mohammad Ghazi's strong header a highlight.
Earlier, South Korea held on to their lead at the top of the pool by drawing 2-2 away to Uzbekistan. The Koreans lead the way on seven points with Iran second on goal difference in the group's other qualifying berth for Brazil 2014.