The Cheltenham Gold Cup winner, which delayed the start of the race after unseating jockey Tony McCoy, had to be put down after later falling at Beecher’s Brook.
A second horse, According to Pete, died after falling at the sixth fence. The National was won by unfancied 33-1 shot Neptune Collonges ahead of Sunnyhillboy.
Synchronised, who got loose before the start but was then cleared to take part, had been tipped to become the first horse to complete steeplechasing’s big-race double in the same season.
The two deaths are expected to raise fresh questions over whether the famous race should be banned. Parts of the course were re-designed for this year following two deaths last year. The annual steeplechase is thought to have attracted 600 million TV viewers around the world as well as £200 million worth of bets.
Earlier, animal rights activists had staged a demonstration against the event. A group of about 30 protesters gathered outside Aintree train station with banners that read: “Don’t Bet on Cruelty.”
Some fences had been modified after a safety review at the course in the wake of the 2011 event, including reducing drops on the landing side.
It is thought another two horses were treated for injuries on the course yesterday.
Fiona Perera, an activist with Animal Aid, said: “The three-day meeting here has killed about 36 horses since the year 2000. We protest especially against the Grand National because of the nature of the course. It is more demanding and the field is an enormous size.”