Two minutes earlier, in a plucky move, Central pulled its keeper in the hope of pressing forward and breaking the deadlock.
Instead it was the home side that attacked down the left flank and got the ball to the impressive Kieran O'Connor.
He dribbled the ball into the circle and threaded it past the remaining defenders for Gilbert to provide the finish.
The pass appeared tantalisingly out of reach until Gilbert closed the space between himself and the ball by propelling his body forward and reaching out with his stick to guide the ball in.
It was a thrilling finish to a game in which Southern had found itself trailing 1-0 thanks to a blistering strike from Dylan Thomas on the edge of the circle in the 18th minute.
Central survived off scraps for most of the game, with Southern dominating possession.
But despite all that time on the ball, Southern struggled to create clean scoring opportunities.
But the weight of possession began to tell in the second spell and the penalty corners started stacking up.
Eventually the home side got the equaliser through Gilbert, whose drag flick found the top right-hand corner.
Despite the win, Southern cannot make the final.
It needed Canterbury to beat North Harbour in the early game to keep its slim chances alive.
Instead North Harbour won 3-2 and is sitting in second place with 13 points.
It shapes as a likely finalist.
Midlands beat defending champion Capital 2-1 in the other men's under-21 match.
It can still make the final if it beats Southern and North Harbour loses to Capital in the final round-robin games today.
Canterbury has already secured a spot in Saturday's final with five wins from six matches.
Southern is in fifth place with nine points and a win against Midlands would cap off a pretty useful tournament.
Defender Johnny Thorn was a rock for Southern at the back, while 16-year-old Malachi Buschl held his own in the midfield against much older opponents. Gilbert scored the goals but O'Connor made a lot of dangerous runs into the circle and created more opportunities.
"I don't think anyone had their best game of the tournament today, but as a team we played some pretty good hockey overall,'' coach Gabriel Rawcliffe said.
In the women's under-21 competition, Southern lost 3-0 to Central and is in sixth place with one win from five games.
Midlands beat Capital 2-0 in the morning games and lead the standings with 17 points.
In the other game North Harbour routed Canterbury 4-1 and is odds on to meet Midlands in the final.
Auckland can still squeak into the final with a win against Central but it will need North Harbour to lose to the winless Capital today.
