The Bombers tabled a four-year contract for Goddard on Monday morning, a deal believed to be worth $800,000 per year, giving the Saints 72 hours to decide whether they would match that offer as Goddard is a restricted free agent.
But the Saints have confirmed in a media release they will not go beyond the three-year contract they have previously offered Goddard, with head of football Chris Pelchen saying the club refused to compromise its pay structure even if it meant losing the 205-game veteran.
"We made a significant offer to Brendon that was relative to both his position and other players within the team," said Pelchen in the release.
"While we are disappointed at his decision to leave the Saints, we are absolutely committed to our 'team first' philosophy in relation to player contracts.
St Kilda Football Club thanks Brendon Goddard for his services to the Saints, which was recently acknowledged with life membership at the Trevor Barker Medal function.
"While we were keen to retain Brendon's services, the club respects his right to exercise his options under new free agency rules."
The Bombers, meanwhile, have been quick to welcome Goddard into the fold.
"Essendon Football Club is pleased to confirm that Brendon Goddard has joined the club after he nominated the Bombers as his preferred club as a restricted free agent," said a statement on the club website."The midfielder has signed a four-year deal that will see him play for Essendon until the end of season 2016."