The Welsh club led through Jordon Mutch's strike before a controversial Samuel Eto'o goal kicked off a comeback from the home side, who went on to win 4-1 after the Cameroonian striker dispossessed David Marshall.
Mackay bemoaned the referee's failure to award a free kick to the visitors but took positives from his side's display, despite suffering their fourth defeat of the Premier League season.
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"We were 1-0 up and [Petr] Cech makes a magnificent save in the top corner from [Peter] Odemwingie’s header to go 2-0 up, and while a top team like Chelsea had a lot of possession against us, there wasn't a lot of pressure on our goalkeeper at that point.
"It was 10 minutes before half-time and that makes a huge difference in the slant of what team-talks can sometimes say, so that obviously is a large factor.
"We were obviously beaten by four but I don’t make any apologies for being beaten by four rather than two, because at 2-1 we had to go and try and press and get back into the game."
The loss was Cardiff's second in a row and they are now just one point above the relegation zone, but Mackay is proud of his players' adaption to the Premier League following promotion last season.
He continued: "I'm very encouraged by the start my group have made and the way they've settled into the Premier League, their competitive nature and the way they've gone at teams. So overall that group can keep their heads held high."