"Disciplinary proceedings have been instigated against... Pedro Neto for unsporting behaviour," a UEFA statement said.
"UEFA's disciplinary bodies will take a decision on this case in due course."
Neto knocked over the ball boy as he ran over to grab the ball late in Wednesday's last 16 first leg, with Chelsea trailing 4-2 at the time.
The incident led to a mass altercation involving players from both teams, and Neto later apologised and gave the ball boy his shirt.
"We were losing and in the emotion of the game I wanted to get the ball fast and I gave him a little push," Neto told broadcaster TNT Sports.
"I'm not like this. It was in the heat of the moment and I want to apologise. I gave him my shirt. I'm really sorry about it - I feel I have to apologise to him."
Chelsea coach Liam Rosenior added: "If there was anything from our side that was wrong or out of order, I apologise on behalf of the club."
Neto, who has scored 10 goals in 42 games in all competitions for Chelsea this season, could face a suspension for next Tuesday's second leg.