But the race was overshadowed as one of the pre-race favourites, Gold Cup-winner Synchronised, had to be destroyed after a fall early in the race.
The winner, a 33-1 shot ridden by Daryl Jacob and trained by Paul Nicholls, reeled in 16/1 Sunnyhillboy in a dash for the line to win by a matter of millimetres as the race was decided by a photo finish.
Starting price favourite Seabass (8/1) came third with Cappa Bleu (16/1) fourth, but as ever the race was marred by a huge number of fallers with several horses still being treated on the track long after the race had finished.
One of those falls led to the deaths of Synchronised - one of the pre-race favourites, ridden by AP McCoy - at Becher's Brook. Another horse, According to Pete, also had to be destroyed after a fall later in the race.
The race had been filled with drama even before the start as Ruby Walsh was injured in an earlier race and could not ride On His Own.
And the build-up took an even more dramatic twist as McCoy was thrown off by Synchronised even before the start, apparently spooked by the starting tape. The horse started the race after being checked by a vet, but fell at just the third fence.
Synchronised appeared to take that fence - Becher's Brook - well, but stumbled thereafter and fell badly.
At the front of the field just a nose separated Neptune Collonges and Sunnyhillboy at the line with Seabass five lengths further back in third place. It was a first National success for both Jacob and champion trainer Nicholls.
"He is class, it is just fantastic," said Nicholls.
Jacob said: "It was very very tough race. I just kept my head down and kept going for all my worth. It was a massive, massive team effort and I'm very glad and lucky to be a part of it."
Neptune Collonges is the first grey to win the race since Nicolaus Silver in 1961.
Seabass, the subject of a huge morning gamble, and Irish amateur rider Katie Walsh jumped the last of the 30 fences in first place but her hopes of becoming the first female jockey to win the famous steeplechase faded as the pair were overhauled.
Sunnyhillboy led with 100 yards to go but an animated Jacob galvanised Neptune Collonges and the pair wore the leader down in the nick of time.