Kapernopylos built a massive stack of 829,500 before the end of play and is now the overwhelming chip leader with nearly 400,000 more chips than current runner-up David Elyashar of Israel.
With only 38 players remaining Kapernopylos has as good a chance as anyone to make the final table of the inaugural event.
Elder, who won EPT San Remo for $1.3 million in April, managed to hold on to third place in chips with 497,500.
Team PokerStars Pro Toni Judet has been one of the most dominant players in this tournament and he finished the day with a reasonable 255,000.
Fellow Team PokerStars Pro Jude Ainsworth survived the day with 233,000 chips, good enough to put amongst the middle stacks.
The number of established pros in the field is beginning to dwindle as Greek players have begun to take over the tournament.
Twelve of the remaining 38 players are Greek and there is also a strong Bulgarian and German presence in the event.
Johnny Lodden, David Vamplew, Kevin MacPhee, Ana Marquez, Roberto Romanello and online poker pro Joe "BigEgypt" Elpayaa were among the notable players to bust on Day 3 of EPT Loutraki. A total of 62 players were eliminated on Day 3.
The money bubble burst midway through the day with Russian Roman Makhlin having the misfortune of getting his pocket kings cracked by an opponent’s Ace-King on the bubble.
The 38 surviving players will reconvene tomorrow at noon local time to go about setting a final table of eight players.
One lucky player will become the first EPT Loutraki winner after the final table on Sunday.
Here are the top 10 chip counts after Day 3:
1. Charalampos Kapernopoylos – 892,500
2. David Elyashar – 503,500
3. Rupert Elder – 497,500
4. Mario Puccini – 495,500
5. Pim Van Riet – 492,500
6. Frederic Hebette – 464,000
7. Zimnan Ziyard – 437,500
8. Panagiotis Koyloykakos – 401,000
9. Andras Kovacs – 362,500
10. Dimitris Mpinas – 362,500