It has been reported that the Argentine swore and made an offensive gesture during a heated confrontation with the match official during the half-time break at the Vicente Calderon.
Simeone was also accused of cornering double goalscorer Neymar in conjunction with club captain Gabi, who was dismissed by referee Gil Manzano for his actions during the interval.
Rojiblancos boss Simeone described the claims as "big lies" during a press conference on Friday but now Atletico have got involved, issuing a club statement not only voicing their support for their under-fire coach but also midfielder Gabi.
"There have been various reports in various media relating to our coach, Diego Pablo Simeone, that are totally false," the Spanish champions claimed.
"Our coach and our captain Gabi have been accused of having cornered and intimidated a Barcelona player in the dressing room of the Vicente Calderon. This information has nothing to do with reality and cannot be confused with any similar act that could have happened.
"It is completely false and from the club will not allow the reputation of our coach and our captain to be stained by such falsehoods.
"In addition, there have also been some images which have created the misunderstanding that Diego Simeone made a dismissive gesture towards the referee.
"Our coach called Jesus Gil Manzano on his failure to award a penalty for handball from a shot by Antoine Griezmann. He does several times and, at the end of the sequence, he touches his forearm touches to reaffirm his complaint. At no time does he make the gesture interpreted by the media.
"Our coach, whenever he has made a mistake, has never shied away from admitting when he has done so. Therefore, we will not accept him being accused of acts that he did not commit and that are completely false."
The second leg at the Calderon was tied at 2-2 when Griezmann's strike appeared to strike the arm of Jordi Alba. The referee waved play on and Barca broke to make it 3-2 on the night, and 4-2 on aggregate.
Gabi was then dismissed during angry scenes at the break, while Mario Suarez was sent off for a second bookable offence in the dying minutes.
However, Arda Turan was also involved in a controversial incident early in the second half when he appeared to throw his boot at a linesman. The midfielder avoided retrospective action over the incident, though, as he was booked by the referee at the time.
