The Argentina striker was accused of being disrespectful towards a number of the opponents in the tunnel after the final whistle of the 2-1 Champions League victory at the Etihad Stadium.
Aguero, who struck the deciding goal in the 93rd minute on Tuesday night, left the Spanish side's players upset with his alleged conduct amid the City celebrations.
Take that: Sergio Aguero celebrates his winner at the death
The ?38million summer signing, who is well known to the Villarreal players from his time with former club Atletico Madrid, took to Twitter to deny any wrongdoing.
He wrote: 'I have no interest in getting involved in controversies, but I have to deny having mocked a Villareal player.
'Everyone can attest to my discipline and professionalism, I wouldn't do something like that.'
Villarreal players briefly clashed with stewards at the end of the game but the row is believed to have continued into the tunnel. The visitors' vice-president Jose Manuel Llaneza said Aguero taunted the opponents.
On the mark: Aguero slots home to secure the 2-1 victory
He said: 'What he has done doesn't say much about the guy. I think it's a lack of respect, ethics and team spirit. I thought he had learned better.
'I don't understand why he would mock fellow players for losing. I'm not saying it because of the result. We lost and we lost, and that's it. Aguero is a player who should thank Spain very much.'
Carlos Marchena, who scored an own goal to cancel his side's 1-0 advantage, said: 'In football you have to have class, especially in times like this. What Aguero did is not acceptable. These situations are a shame and are a mark of the man who does it.'
On his player's anger on the pitch, Villarreal manager Juan Carlos Garrido said: 'The players were emotional. They thought the goal was offside. It wasn't.
Anger: Villarreal players were furious with the ref at the final whistle
'I think we have done a good match and we did deserve - if not to win - a 1-1 (draw). 'I thought we had a good match in general, in all aspects, and to lose in the last minute inthis way is difficult.
'Congratulations to City because they won but we thought we deserved more from this match.'
Meanwhile, Roberto Mancini claimed City can still win their Champions League group. With Bayern Munich and Napoli drawing 1-1, the German side look favourites to top the group, with City's game in Italy on November 22 beginning to look like a straight shoot-out for second place.
Mancini said: 'That is a very important game for us now. We will play in Villarreal in 15 days but the game in Naples will be the crucial game. It is still possible to win the group. It is open now.
off you go: Roberto Mancini removed Adam Johnson early on
'We were lucky to win this game. Any team that scores so late is lucky. But we had enough chances to win and eventually we did. It would have been very difficult if we had lost this.'
Villarreal opened the scoring in the fourth minute, forcing Mancini into a tactical change, with Adam Johnson being substituted. City equalised through an own goal soon after.
Johnson looked unhappy to come off and Mancini said: 'We were conceding four or five counter-attacks and didn't have many players in the middle.
'I wanted to move Yaya Toure behind Edin Dzeko. Adam played very well but it was a tactical substitution. I spoke with him and he understood. Players have to go off and will be disappointed, but Adam is a very important player for us.'
Source: Daily Mail
Source: Daily Mail