New signing Samuel Eto'o started and Demba Ba was a second-half substitute, while Fernando Torres failed to make the bench as midfielder Oscar scored.
Mourinho claimed responsibility for the defeat and he promised to work hard with the team.
Cameroon striker Eto'o made his home debut after joining from Russian side Anzhi Makhachkala, but did not test Basel goalkeeper Yann Sommer until injury time at Stamford Bridge.
Fellow forward Ba was introduced before Basel's second goal as the Blues searched for a winner, while £50m signing Torres was not named in Mourinho's match day
squad.
Chelsea dominated possession in the opening hour against Basel, but created few goal scoring opportunities apart from Oscar's opener.
They were punished by the Swiss champions as impressive winger Mohamed Salah leveled with a curling shot before skipper Marco Streller headed in a late winner.
Basel's victory ends a run of 29 Champions’ League group games without defeat for Chelsea at Stamford Bridge.
Mourinho believes the Blues will have to beat Basel in the return fixture on 26 November to "compensate" for their home defeat.
"We lost three points that we must get somewhere," said the Portuguese. "We must get them, in Basel, or Schalke, or Bucharest, or all of them or some of them.
"Normally you have to win the matches at home and get a few points away. Now we must win six points at home, Schalke and Steaua, but we have also to win points away.
Basically, the objective of finishing in the top two in the group phase and to go to the next stage of the Champions League is an objective that is not lost - far from it.
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