The confrontation escalated on Monday when Arokodare stood his ground on the training pitch rather than leave, prompting Peixoto to abandon the session altogether.
Wolves responded by drafting in extra security at their Compton Park base the following day to keep the 25-year-old away from first-team facilities, an early and public test of authority for the Portuguese head coach less than six weeks into the job.
Arokodare, who spent last season with Wolves as they were relegated from the Premier League, has not travelled with the squad for this evening's pre-season friendly at Maidenhead. He also missed the start of last week's warm-weather training camp in Portugal, only being called up late following an injury to fellow forward Adam Armstrong.
The Nigerian faced disciplinary action in April after a physical altercation with team-mate Mateus Mane following a 4-0 defeat by West Ham, and scored three Premier League goals in a difficult campaign.
Peixoto, who joined from Portuguese club Gil Vicente in June, has made clear he intends to run a tight ship at Molineux.
Speaking in his first interview since taking charge, he said: "Firstly, I'm a very demanding coach. But, I believe in giving others maximum freedom and maximum responsibility. I want us to work as a team and as a unit and build a good environment. This is important to me, but I know very well what I want from the team. I want my team to be organised with and without the ball.
"Secondly, I want a team with intensity and to be aggressive and win duels. The third one is I want to show the quality of the players. To play an offensive game and to try and press high. To try and be the main character of the games. I want to win games, but I want to win while playing good football. With passion and energy.
"[The supporters can expect] a team with ambition. A strong character and identity and a strong idea of the game. A team that never gives up to win three points and to try and make the fans proud."
Arokodare joined Wolves from Belgian side Genk last summer and has been keen on a loan move to Torino, though that switch has stalled, while Genoa have also made an enquiry over his availability.
Peixoto is understood to be in the market for a new forward of his own despite having already brought in Raul Jimenez this summer, with Wolves previously linked with Middlesbrough-bound striker Will Lankshear before turning their attention elsewhere.
With the disciplinary situation now public, Wolves face a delicate balancing act in trying to move Arokodare on before the transfer window closes while managing the fallout inside the dressing room.