The third goal came from centre-mid Callum McCowatt in the 52nd minute.
Frankly, the margin of defeat could have been wider after City foragers fired shots that clipped the woodwork before ricocheting out of harm's way, to the relief of the Bluewater faithful.
Credit must also go to Bay United goalkeeper Mack Waite who again stepped up after regular glove man Ruben Parker Hanks didn't receive the all-clear from the medical staff for concussion picked last month despite his name appearing in the official squad list yesterday.
Waite thwarted numerous opportunities as the visitors mounted waves of attacks at will.
Whatever scant possession the hosts got was frustratingly lost with inaccurate passing. In defence of coach Brett Angell the new faces and out-of-position players, such as Birhanu Taye in the backline, suggested it wasn't going to be a pretty picture in a summer when wins at home have proved elusive.
The city slickers simply had too much time, space, territory and possession for the hosts, who have now lost any sliver of a mathematical chance of making the playoffs with three rounds to go.
City's individual skills and sixth sense - built on the foundation of simplicity through passes and use of width on attack - slowly, but surely, stifled Bay United.
Continuity is something that Auckland coach Ramon Tribulietx has worked on.
"It's our style and we practise it every day at training," said Bilen, lauding Tribulietx for patiently building a tensile template over several years.
"They say there are no good players in this country but you can always find them if you know what you're looking for.
"All they need is hard work, good coaches and good education," he said, adding he was "super happy" with Tribulietx who was injecting youngsters, such as McCowatt, into the squad.
But Bay United also value Angell's injection of fresh talent with the likes of Jorge Akers, Ben Lack and Jordan Lamb, who would have relished game time against City.
"It's an amazing feeling because it's my first year in there," said Lamb, a 62nd-minute substitute who had the first shot on target for Bay United in the second minute of added time.
The 18-year-old striker/midfielder from Taupo, who played for Waitakere United youth for two summers, thanked Angell for the chance and was hoping to learn more from him.
Lamb came into the squad during the January transfer window.
"I've never wanted anything more than to play in this league when I was younger so it's just great experience to be here to play against players such as [Albert] Riera who have played for the [Wellington] Phoenix and the A-League as professionals."
Always hungry for more, Lamb said he wanted to improve his game in a bid to gain promotion to the higher echelons.
He played half a game away against Tasman United and got on the park for 15 minutes against Eastern Suburbs.
Lamb hadn't missed the gulf that Auckland City exposed in the premiership with their world-class pedigree.
"It's a massive thank you to Brett for giving me a chance to play right to the top level and beyond my age."
Bilen was expecting a torrid battle against Tasman United in Nelson this weekend after the latter lost 3-0 to Eastern Suburbs yesterday.
Bay United host the Canterbury United Dragons at home this Sunday in a 2pm kick off. The Dragons posted a come-from-behind 5-3 victory over the Wellington Phoenix Reserves yesterday.
