Erik Pieters was penalised for bringing down Samuel Eto'o just outside the penalty area in the 28th minute of the fourth-round clash, and Oscar sent the resulting set-piece curling into the top left-hand corner of Asmir Begovic's net.
The hosts hit the post twice thereafter, but the Potters boss believes the decision to award Eto'o a foul was a pivotal point in the match - though he remains pleased with the effort his side showed to try and lead a fightback.
"Obviously it was a fantastic strike, but I didn't feel it was a free-kick," he told ITV.
"We couldn't quite create enough clear openings," he continued. "They are very adept on the break, so it was difficult for us, but I'm pleased with what we did.
"We stuck at it and didn't go under, made sure we were resolute, blocked shots when we had to, had good defensive awareness and tried to go the other way as well.
"We're disappointed to go out of the cup obviously, but there were more positives than negatives I would suggest."
Chlesea's reward for their win is a fifth-round tie at Manchester City, while Arsenal host Liverpool as the Premier League top four all face off in the pick of the ties.