The council failed to repossess the Edgar Street ground late on Thursday and issued proceedings in court on Friday morning.
Club chairman Andy Lonsdale said a payment and apology were made earlier.
The council confirmed it had received the outstanding sum, thought to be about £50,000
In a statement, the authority said it had "issued proceedings in the county court against Hereford United (1939) Limited for forfeiture of the leases and repossession of the ground".
"These proceedings were subsequently served on HUFC directly," he said.
"In response to this action, we can confirm that HUFC has paid outstanding sums due to the council."
The council said it was now consulting with its legal team.
Hereford United was thrown out of the Football Conference in June over unpaid debts and a petition to wind the club up has faced a string of adjournments in the High Court.
Mr Lonsdale apologised to fans for "the turmoil this is causing".
"We are wholly committed to producing a good level of football at Edgar Street," he said. "We will strive to get this football club back on an even keel.
In September, the council joined the HM Revenue & Customs court petition.
It said it decided to step up its action against the club when a hearing was adjourned for a seventh time on Monday.
"In light of the further six week adjournment, we decided to use other legal actions available to us as landlord," Councillor Tony Johnson, leader of the council, said.
He said on Thursday council staff were sent to take possession when they believed it would be empty, but assistant manager Neil Phelps was on site and refused them entry.
Mr Johnson said his aim was to enable a new owner to "make sure we've got continued sport on that ground".
"We want somebody in there that is doing what the terms of the lease and contract say," he said.