Porto skipper Maicon delivered the knockout blow in the second period after Andre Andre and Willian, who scored from a direct free-kick for the third game running, traded first-half strikes.
Defeat was Chelsea’s fifth of the campaign – they only lost four throughout the whole of last season - - and leaves the Blues third in Group G with second-placed Dynamo Kiev their next European opponents on 20 October.
“I got the performance, if I forget two ridiculous mistakes. Unacceptable mistakes,” said Mourinho. “Apart from that the team played well and had good reactions to both goals conceded. They had desire, the performance was not bad.
“When you win matches and perform well, it is easy to know your best team. When the team is not winning on a regular basis it is normal that you have to make changes. After games like tonight it is difficult to analyse.”
Porto opened the scoring in the 39th minute when midfielder Andre powered home a rebound from goalkeeper Asmir Begovic’s parry, before Willian curled a free-kick over the wall and beyond former Spain No1 Iker Casillas in the final act of the first half.
Chelsea’s defensive frailties were again exposed seven minutes into the second period when Brazilian defender Maicon evaded Ramires to plant a near-post corner past Begovic.