The Blues went 1-0 down after 39 minutes as Andre Bras Andre gave the hosts the lead after Chelsea failed to clear their lines following Asmir Begovic's save from Yacine Brahimi's shot.
Brazilian winger Willian drew Mourinho's side level with a brilliant free-kick just before the break.
But shortly after the restart, captain Maicon headed in at the near post as Chelsea's defence were left ball watching.
And Mourinho - who won the Champions League with Porto in 2004 - conceded that they way they lost to the Portuguse side was "ridiculous."
GETTY
Jose Mourinho's side lost 2-1 on his return to his former side
"We watch dozens and dozens of repetitions of Porto taking corners," he said. "We were completely ready for that and in a moment when the game is under control we concede a goal that is ridiculous.
GETTY
Mourinho's starting XI - John Terry, Eden Hazard and Nemanja Matic were all dropped to the bench
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"They hit the post from a similar mistake. Apart from that the game was balanced. Two ridiculous moments and we were punished."
Chelsea now lie third in Group G as Porto move top.