Despite holding a 1-0 half-time lead at Prenton Park, the Blues lost control after the break and succumbed to a damaging second defeat in four days.
Having been eliminated from the Champions League by Barcelona with a semi-final loss on Saturday, Chelsea are six points below WSL leaders Manchester City with a game in hand and eight goals to make up.
“I think the title is done,” said Hayes, whose side have three matches left to play.
“Of course, mathematically it’s not, but I think the title is done. Our job between now and the end of the season is to keep pushing until the end, but I think it will be very difficult.”
Aggie Beever-Jones’ ninth-minute finish had put Chelsea ahead – and seemingly on course for a routine win on the road as they eyed a fifth straight WSL title.
But Liverpool, who came into the match on the back of a 10-day break, turned things around to stun the second-placed side.
Sophie Roman Haug levelled to spark a topsy-turvy last 40 minutes as Gemma Bonner’s injury-time header – her second of the game – clinched the three points for Matt Beard’s side.
“This team has done a tremendous job in my time here to really compete and push for titles,” added Hayes.
“I don’t know if we have ever conceded four goals in a half before – three from set-pieces is just unforgiveable.
“But I’m going to credit Liverpool. They wanted it, they executed their gameplan. They delivered from that and from set-pieces they got goals.”
When Hayes announced in November she would be leaving Chelsea at the end of the season to take charge of the United States women’s national team, they still had a chance of finishing 2023-24 with a historic quadruple.
But since their League Cup final loss to Arsenal on 31 March, they have been eliminated from both the FA Cup and the Champions League at the last-four stage.
“We looked exhausted but I don’t make excuses,” said Hayes. “I want to remind our fans how much success we have brought over the years.
“It’s not to be this year but I’m sure Chelsea will continue to be at the top of the game and it’s important that we go out in the best possible way.”
Despite being disappointed with how the last month has panned out, 20-year-old winger Beever-Jones said Chelsea would fight until the end.
“No other club in our league is playing in four competitions like us,” she said. “Arguably you can say that showed today, but we’re Chelsea and we want to be in four competitions. We still put a battle up that we can be proud of.
“It’s not over yet, there are still three games of the season and we’re not written off just yet. If teams want to write us off that’s fine. We can have this conversation when the league is done and we’ll see what the outcome is.”