The 28-year-old cut a dejected figure on the interchange bench after hurting the foot again and was consoled by coach Alan Richardson from the coaches' box.
He was playing in just his third AFL game after returning from the injury, which had robbed him of much of the season.
St Kilda said further action around the injury would be determined after Gilbert met with a surgeon.
Top-eight Tigers too good for Saints
Earlier this season, he spent nearly three months in a moon boot after the stress fracture on his fifth metatarsal bone in his left foot flared up again.
He initially broke down with the injury in the pre-season in early February and had surgery.
He said recently he wasn't sure what caused the fracture and that it could have been something as innocuous as the type of shoes he was wearing combined with hard training surfaces.
He played in the first three rounds but the injury became aggravated against West Coast in round three and it was thought he would miss another month.
But subsequent scans later in April showed the fracture had failed to mend and he was ordered to keep resting it completely.
He returned via the VFL on August 2 before gaining a call up to the Saints' side that played the Western Bulldogs the following week.
Gilbert is contracted to the club until the end of next season after signing a three-year extension in 2012.
