Well, actually, and no one remembers this, there has been a replay in FIFA World Cup qualification before, but under slightly different circumstances. For the last world cup, Bahrain and Uzbekistan played each other for the right to face Trinidad and Tobago and it's safe to say murky dealings were afoot. The Uzbeks won the first leg 1-0, but during the match the ref made a big blunder. He correctly gave the Uzbeks a penalty, but an Uzbek player encroached as/before it was taken (and scored), and then the ref made a catastrophic error - he awarded an indirect free kick to the Bahrainis, when legally he should have ordered a re-take of the penalty. The Uzbek players pointed this out to him at the time, but he ignored them, so they pointed it out at the end of the game. The whole situation escalated and FIFA decided to replay the whole match (also delaying the second leg). Bahrain drew the replay in Tashkent 1-1, and then in Bahrain it was 0-0, so they (Bahrain) went through.
It ended up looking like the most spectacular fudge and it's hard not feel for the Uzbeks who were cheated out of a 1-0 (and pretty much 2-0) lead. And the right to face Trinidad and Tobago for the last berth in the World Cup.
http://www.fifa.com/worldcup/archive/germany2006/news/newsid=27212.html