Luiz and Higuain came together as the Blues were put through their paces at the Olympic Stadium in Baku on Tuesday night.
Higuain appeared to challenge the Brazilian from behind, angering Luiz and causing the defender to lash out with his arm.
The pair exchanged words as captain Cesar Azpilicueta came over to intervene, while manager Maurizio Sarri appeared to be infuriated by their actions.
The Chelsea manager stormed off the pitch towards the dressing room, throwing his cap on the floor and kicking it on more than one occasion while angrily gesturing towards his players as Higuain looked miffed while talking to Pedro as he approached the tunnel.
Sarri left Gianfranco Zola to finish off the open training session, with the Italian boss too disgusted to continue drilling his players.
The altercation, which left Luiz fuming on the touchline, is hardly the best preparation for Wednesday night’s clash with Arsenal.
It is not the first time Sarri’s authority has been questioned, with Kepa Arrizabalaga refusing to be substituted during the Carabao Cup final against Manchester City.
The bust-up comes amid reports the manager will leave Chelsea for Juventus, having agreed terms with the Italian giants.
Kante took part in the open training session but underwent drills on his own before heading down the tunnel early – potentially for more treatment and an assessment.
Speaking about Kante in his pre-match press conference, Sarri said: “He had a little problem on Saturday, a very little problem with his knee. It’s not really a very serious injury.
“The problem is the timing because we had only four days to try to recover him. We are trying. At the moment we don’t know. We will try until the last moment. We will try tomorrow, but at the moment we don’t know.
“He is 50/50 at the moment. Yesterday 60/40 for the no, today 50/50. He was a little bit better this morning.”
Meanwhile, Sarri was tight-lipped about the chances of Olivier Giroud starting the final against his former club.
The striker is top scorer in the Europa League this season with 10 goals but is not guaranteed a starting spot, although Higuain’s spat with Luiz may have increased the Frenchman’s prospects.
“I need to consider him, first of all,” said Sarri on Tuesday.
“He has played very well in the Europa League and scored a lot of goals. In this competition Olivier was very important for us.
“I have to decide tomorrow, but I have to consider him I think.”