The Nomads made it back-to-back titles with their 2-0 win at Penybont, which meant the The New Saints' 2-0 home win over Bala Town with 10 men was redundant.
Limbrick, who has only been in the role six weeks after replacing Scott Ruscoe, admitted the hurt and disappointment was palpable at Park Hall.
The new head coach praised the way his 10 men earned a victory over Bala, following a contentious early red card for Ryan Harrington, but quickly turned his focus to how the Oswestry side will recover for next season.
"It hurts, there's no doubts about that. I know when coming here, and the players know - you can see in the changing room there - they're disappointed because of the overall result," said Australian Limbrick.
"We know here you need to win titles, win leagues, and we'll be straight back at it after a small break in the off-season.
"We'll be back on it to win it next season, that'll be our challenge and our goal and target."
Ben Clark had already given Saints an early lead before Harrington's 20th-minute dismissal. Adrian Cieslewicz struck early on in the second period to wrap up the points.
But goings-on elsewhere meant the title would remain at Deeside with Connah's Quay, who struck after just four minutes at Penybont and despite some nervy moments sealed the win through former Saints man Aeron Edwards.
TNS' eight-year grip on the Welsh top flight has been well ended by their Flintshire rivals, whose second title in a row means the Saints will enter the new UEFA Conference League early next season.
Limbrick said: "We're disappointed we didn't win it, there's no doubt about. however I can only commend the players for how they went about their work today.
"It was a dubious sending off early in the game and for them to score two and keep a clean sheet and have a really positive second half was everything we asked of them.
"Since that 0-0 draw against Connah's Quay, where we knew it was out of our hands, the players have been utter professional, worked hard and got the results we wanted.
"We've won 3-0, 3-0 and 2-0, we couldn't have done much more than that.
"We slipped up in a couple of games, but we couldn't have done much more today, the performance was very good.
"Ryan Harrington gets himself in an awkward position and pulls the player back but Keston (Davies) is close enough to ensure it's not an obvious goalscoring opportunity."