Iranian captain Javad Nekounam, who plays in Spain for Osasuna, scored the first goal in the 17th minute at Tehran's Azadi stadium with a dazzling strike from outside the penalty area.
The second goal hit the Kuwaiti net in the 93rd minute after a stray ball was shot in by Gholam Reza Rezaei who benefited from some extraordinary confusion in the Kuwaiti defence.
The result leaves Iran atop Group 5 in Asian qualifying with 12 points, making up for the lacklustre start to its campaign earlier this year and giving under-pressure new coach Ali Daei some breathing space. Iran had already qualified for the next stage before this match, which was its third successive win after three draws.
Daei, who holds the world record for international goals, will be hoping to make his finals coaching debut in the 2010 FIFA World Cup after playing in the 1998 and 2006 FIFA World Cups.
The final qualifying round is scheduled to begin in September between 10 Asian countries. Asia has four automatic berths in the finals in South Africa in 2010 while the fifth-placed side play off against a team from Oceania.