The match was marked to honour the memory of former Sheffield United defender George Baldock, who passed away earlier this month.
Baldock had moved to Panathinaikos in the summer and passed on October 9 at the age of 31.
Before kick-off, Panathinaikos players trained in shirts with Baldock's squad number of 32 on them, while Chelsea players also held up a shirt bearing his name and number. Both sets of fans also held up placards with 32 on them.
Once the match kicked off, Chelsea were always in control after Felix put the visitors ahead on 22 minutes. The goal was created by Mykhaylo Mudryk, who also laid on Felix's second after halftime.
The winger scored himself before the break, while the game was wrapped up via Christopher Nkunku. Panathinaikos scored midway through the second-half as former Manchester United winger Facundo Pellistri found the net.
But Chelsea were always in control and leave Athens maintaining their 100 per cent record in the competition.