Adroit Solomon Islander Fa'arodo swiftly followed up to tap it into the goal at the near post as the gobsmacked Bay defence were reduced to spectators - another summer allergy.
Bay golden boot contender Sean Lovemore lamented: "It's a thing of the old. It's something like 14 or 15 times we've gone a goal behind but managed to claw it back. Unfortunately, not this time."
In keeping with tradition, Lovemore almost nodded in the equaliser in the 32nd minute but for a fortuitous deflection.
However, Wellington defender Tim Myers conceded a penalty kick when referee Campbell-Kirk Waugh deemed him to have brought down Bay captain Ross Haviland in the 18m box from the ensuing cornerkick.
Englishman Saul Halpin calmly pushed it past goalkeeper Michael O'Keefe from the spot to make it 1-1.
It wasn't until the 78th minute that Fa'arodo struck again, latching on to a ball threaded through the right wing before slipping it past Hill from an oblique angle to give the men from the capital a 2-1 lead, which they kept intact to the end.
Lovemore felt 1-1 would have been a fair result but agreed Wellington had the class to find the edge in the last 10 minutes.
"You know, with the kind of players they have in their locker we can't afford to switch off because we'll get punished."
He agreed Bill Robertson, Tim Meyers, Aaron Scott and Ian Hogg had put him in a straitjacket.
"I'm not too happy with my game but I think they've done a pretty good job of marking me," Lovemore said, believing he wasn't in the game for 70 to 80 minutes.
It did beg the question if Bay United had a plan B to ease the attention on Lovemore.
A simple but effective ploy would have been to put the ball out wide more on the flanks to stretch Wellington's backline before threading or curling crosses with some urgency to enable Lovemore to pounce on them.
Left wing Viktor Lekaj did but his crosses often lacked purpose or intensity. Too often Bay tried to force passes through the middle where yellow shirts had pitched up tents.
In reality, it was a game between men and boys where the visitors were outmuscling a youthful Bay.
Wellington striker Phil Ifill was a shadow of his Wellington Phoenix form and should have come off the bench for a side that will need to play much better against Auckland or in the O-League.
Lovemore said: "I don't think we played badly at all. In parts, in the second half, we were actually controlling things at times."
The focus has shifted to "giving it all this Sunday" in the capital city in the away leg of the semifinal.
Bay would need to score at least two goals and win to make the final against favourites and minor premiership champions Auckland City who beat Waitakere United 2-0 at Fred Taylor Park on Saturday.
Ryan Tinsley, serving a one-match suspension, returns to stoke the fire in the engine room.
Wellington co-captain Cole Peverley hailed his "talented and experienced" troops.
"We were playing well but they got back into the game with a pen [penalty] which, to be honest, wasn't one," he said.
"He [Haviland] screamed before he fell so that tells the full story.
"We gave them a chance but the boys got on with it so, to be honest, we fully deserved to win it."
Peverley said Wellington were beginning to return to their post-Christmas best.
Fa'arodo and Luis Corrales, requiring stitches to a head wound, were "weapons".
"You look at our bench and we have Jarrod Smith, Cory Chettleburgh, Pat Fleming, Michael Gwyther are all very good players so with that depth the boys stepped up today."
Lovemore was "dangerous" so the plan was to "cut him out of the game", Peverley said, crediting his Beefeaters for putting up the storm shutters.
