He had been playing for Sunderland until the start of his trial but was sacked after changing his pleas and admitting two charges on the first day.
“The club only became aware of the change of plea on the first day of the trial,” it said in a statement.
“Had the club known that Mr Johnson intended to plead guilty to any of these charges, then his employment would have been terminated immediately.”
Johnson had denied all four charges he faced up until the start of his trial. After admitting to two offences, he was found guilty on one count and cleared of the fourth.
However, the trial at Bradford Crown Court heard evidence that the club’s chief executive, Margaret Byrne, met with Johnson and his barrister in May 2015 where he accepted he had kissed the girl and exchanged messages with her.
Johnson continued to play for the side despite those admissions, the court heard.
The player had been initially suspended by the club following his arrest in March 2015 but that was lifted two weeks later.
Following the end of the trial on Wednesday, Sunderland issued a statement which said Byrne was only “present during part of that meeting” in May 2015.
The Premier League club also denied they “knew all along that Mr Johnson was intending to change his plea just before trial to enable him to continue to play football for the club and that the club may also have been involved in tactical discussions about the plea”.
The statement added: “This is utterly without foundation and is refuted in the strongest possible terms.”