Auckland City went 1-0 up in the eighth minute after a passage of play from a side that is savvy on an international platform.
The possession came from a Sean Liddicoat blunder midway in Bay United's half. That's all Auckland striker Micah Lea'alafa needed to turn and drive into the top of the penalty area before swivelling to lay it back to central midfielder Clayton Lewis, who had plenty of time to curl it past diving goalkeeper Joshua Hill on his right-hand corner.
The visitors came close to scoring again four minutes later when right back Kim Dae-wook timed his header from a corner with precision to the left upright but, fortunately for the hosts, right back Fergus Neil was stationed there to chest it down and clear it away.
A couple of vociferous fans should take credit for exposing Bay United's mindset minutes before halftime when they yelled: "Get in there!"
Kilkolly reacted immediately with some aggressiveness but it wasn't until the 44th minute that Bay United created an opportunity.
Teenage centre-mid Ross Willox showed a turn of feet when he intercepted a pass just inside his half, skilfully skinned his counterparts through the spine of the field before 25m out finding striker Saul Halpin on the left flank. But Bay top scorer Halpin, whose father Russ has been in the province for 10 weeks following his stint, frustratingly didn't back himself to have a shot as his oblique cross was deflected over the goal line.
However, from the ensuing corner from Willox, Lea'alafa fouled midfielder Facundo Barbero just inside the top of the penalty area. Referee Matt Conger pointed to the spot two minutes into added time.
Auckland keeper Enaut Zubikarai Goni dived to his right but stuck his foot out to the left to deflect the ball to deny Kilkolly a goal.
Whatever acting coach Jamie Dunning, at the helm as coach Brett Angell serves his four-match suspension in the hospitality booth, said in the changing rooms worked wonders in the second spell.
The Finlay Milne-skippered side came out with more of an attacking mindset and almost equalised in the 56th minute after Lewis grabbed a runaway Barbero from behind.
Referee Conger flashed yellow cards to Barbero, Auckland striker Ryan De Vries and ex-Phoenix defensive midfielder Albert Riera in the next few minutes.
Barbero had a blinder and became a target of fouls.
The parochial fans were on their feet in the 72nd minute when centre back Martin Canales Ramos provided the scaffolding to move the ball to Kilkolly, who relayed the pass to Mason-Smith. The striker turned captain and centre back Mario Bilen inside the box to leave keeper Goni grasping at thin air for a 1-1 equaliser.
A misdirected back pass towards their own goalmouth saw Bilen shadow the ball as Mason-Smith stayed on his heels but the centre back lost his footing and the Bay striker pounced on the ball.
Mason-Smith's lob-wedge shot past an advancing Goni must have felt like a slow-motion nightmare to Auckland coach Ramon Tribulietx and his men on the bench as the hosts shot to a 2-1 lead in the 89th minute.
Tribulietx gave his skipper a mouthful before the restart as the defender remonstrated with the referee for a foul.
The final whistle sent fans and players into wild celebrations.
Tribulietx lamented his troops' inability to capitalise on more opportunities to go up 2-0 in the first half.
"Then they had a penalty, probably the one opportunity close to the box," he said.
The Spaniard said in the second half with the the wind in their faces Auckland found Bay United pushing higher up making it harder for them to settle down.
"We could have sealed the win with an open chance in front of the keeper but, basically, on the counterattack they got a second goal," he said of substitute Harrison Moss-Edge missed another chance inside the box in the 87th minute although pivot Emiliano Tade also did everything in the 83rd minute but his ensuing strike went begging past the the right upright from an ibtuse angle.
Tribulietx shrugged his shoulders and said his players simply had to come back from the loss.
Asked if he thought Mason-Smith had brought down Bilen from behind, he replied: "No comment."
Tribulietx said the long trip to Hong Kong could have resulted in fatigue but he refused to offer any excuses.
"It looked like we were a little bit lethargic at times but it's happening to us this season - we don't put games to bed.
"The games have been punishing us, you know, other games where we've been 1-0 on top."
He said heat wasn't a factor as it was the same for both sides.
Auckland City have two games in hand and still have the chance to rocket to the top of the premiership table from fith place.
"It's not over. We're disappointed because we haven't managed to get enough points to be clearly on top but we have to get up into our normal gear with seven more games to play."
Bay United jump into fourth place to sit two points below leaders Waitakere United on 25 points while Team Wellington and Eastern Suburbs, both on 24 points, occupy the second and third rungs.
While Bay United played as unit, Barbero and Willox were outstanding and didn't seemed to be battling stage fright in a televisied game.
Goalkeeper Hill, no doubt, remarkably maintained his standard throughout this summer.