A Newcastle side set up to frustrate Chelsea held Maurizio Sarri's visitors at bay for 76 minutes until referee Paul Tierney pointed to the spot following Fabian Schar's challenge on Marcos Alonso, allowing Eden Hazard to open the scoring.
Replays suggested Schar had got a foot to the ball, but Newcastle responded seven minutes later through Joselu's near-post header, benefiting from some fortune of their own, with DeAndre Yedlin appearing to foul Olivier Giroud in the build-up.
However, Yedlin inadvertently turned Alonso's first-time strike into his own net to gift Chelsea the points, leaving Benitez to reflect on a contentious decision amid questions over his tactical approach.
"Obviously, we wanted to stay in the game and take our chances and we were very close," Benitez told Sky Sports.
"The penalty is soft, the foul was soft and then maybe they could have scored at the end. These two situations, we were very close."
Asked about his approach against a team Newcastle beat 3-0 in last season's corresponding fixture, Benitez said: "We knew that playing open against them, with their pace and quality and ability would be very dangerous, so we needed to be sure we were compact to frustrate them and beat them if we had our chances.
"The penalty changed everything, we had to be more open and we scored a goal but we were still so open that maybe they could have scored with two or three counter-attacks. They scored a goal from a soft foul and a second ball from a free-kick and we have to be more aware to that.
"Everybody knows that in the last 10 minutes, the chances that they had, they were very dangerous. So that is the reason why [we defended]. They are a good team and candidates for the title."
Newcastle were without captain Jamaal Lascelles and midfielder Jonjo Shelvey through injury, though neither player is expected to be out for long.
"Jamaal has an ankle problem but is working with the physios," Benitez added. "Jonjo is one or two weeks."