A late own goal from DeAndre Yedlin saw the Magpies slide to defeat, moments after substitute Joselu had drawn the home side level following Eden Hazard's controversial opener from the penalty spot.
The former Liverpool and Chelsea chief frustrated Maurizio Sarri's side for the majority of Sunday's game, employing a deep defensive backline designed to subdue their more illustrious opponents.
Benitez claimed the setup was designed to keep his side competitive, before the Spaniard questioned Paul Tierney's decision to award Chelsea a penalty when speaking to Sky Sports.
"We wanted to stay in the game and try to take our chances. We were very close but the penalty was soft, the foul was soft.
"Maybe they could have scored at the end with the quality they have on the counter-attack but, no, these two situations. It's a pity because we were very close.
"We knew playing open against them, with their quality and ability, they can beat players in one-versus-one situations. Between the lines, they are very dangerous.
Benitez believes the penalty award changed the game, but admitted that his side's late lapse in concentration had ultimately cost his side dearly.
"We needed to be compact, maybe we could frustrate them into mistakes and we'd have chances. The penalty changed everything and we had to be more open.
"We scored a goal but we were so open they had two or three counter-attacks. If they scored from one of these chances, fine, but they had a soft foul and a second ball from a free-kick where we needed to be more aware."
The Newcastle boss will hope to welcome back a number of first-team players back into the fold next weekend, after captain Jamaal Lascelles and Jonjo Shelvey were forced to watch on from the sidelines through injury.