Mohamed Salah's solitary strike with three minutes remaining gave the Swiss champions their second win over the London club in this season's Champions League, although Chelsea still clinched their place in the last 16 thanks to Schalke's goalless draw with Steaua Bucharest in Romania.
That meant it was job done for Chelsea, who came to Switzerland with the aim of ensuring qualification with a game to spare in Group E, but Mourinho was unable to muster a smile after watching a substandard performance.
"We don't go through because we got a result, we go through because Schalke did not get a result, and for me it's not the same," said the Portuguese.
"In the end, we qualified, which is our first objective, and now we have the last match at home to get the result to finish first," he added, with Chelsea knowing that a win at home against Steaua on December 11 will guarantee them top spot and secure, in theory, an easier draw in the next round.
Mourinho was quick to praise Murat Yakin's Basel side for their display - which followed a 2-1 victory in London in September - but he acknowledged that his decision to make just one change to the team after Saturday's 3-0 win at West Ham was wrong.


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