The Swiss league champions completed a Group E double over Chelsea with a vital 1-0 victory on Tuesday.
Overcoming a Mourinho-coached outfit twice in as many meetings was particularly pleasing for Yakin.
"To win twice against Chelsea is something historic," Yakin told reporters.
"But we have now played four times against them and are therefore not awestruck.
"I'm very happy for the team and for all who witnessed it in the stadium, but that Mourinho has had to congratulate me twice is already something beautiful."
Mohamed Salah scored an 87th-minute winner at St Jakob-Park, giving Basel a result their coach felt they deserved.
Yakin said his team were the better outfit in the second half but believes Chelsea always looked threatening.
"We fought for every blade of grass. In the second half we controlled play, it took several attempts but in the end it worked out," he said.
"It would have been undeserved had we not won or even lost, which can happen against an efficient Chelsea.
"The supporters pushed us over the 90 minutes to the end - they wanted us to win just as much as we did."
Yakin, whose team are second in the group after the win, paid tribute to goalscorer Salah, whose neat first touch and nice finish gave Basel victory.
"We are glad that Salah is with us, he builds up a lot of attention when he is in top form. He's an attraction," he said.
