He pulled it out, but Ruslan Ponomariov didn't make it easy! The first rapid game was drawn, and then Gelfand won game 2 with White. When game 3 was drawn as well it looked like it would be over, as Gelfand only needed to draw with White to close it out. It didn't happen: Ponomariov sacrificed the exchange and his bishop pair carried the day. On to blitz, where Gelfand won with White after a Ponomariov blunder, only to blunder right back in the next game. On to another blitz mini-match, and again Gelfand won first with White. This time he held, winning with Black as well, and by a 7-5 overall score became the 2009 World Cup champion. (The games can be found here, but I'm not going to annotate this batch.)
So, congratulations to Boris Gelfand! It was an impressive performance, not least because the guy's no spring chicken at the age of 41. Youths, beware of old age and treachery!
This means that he qualifies for a Candidates tournament that will consist of the following players:
Gelfand (World Cup champ).
Aronian (Grand Prix champ).
Kamsky (loser of the 2009 candidates match to Topalov).
Topalov or Anand (whoever loses the world championship match next year).
Carlsen and Kramnik (probably, based on the averages of their July 2009 and January 2010 ratings).
The runner-up of the Grand Prix (as yet undetermined).
Any 2700+ player the organizers decide to invite.
(More details here.)