Yakin's men fell behind 17 minutes into the UEFA Champions League Group E match when Federico Piovaccari got on the end of a fine ball from Lukasz Szukala to fire home.
Basel looked set to suffer frustration in their bid to force a leveller, but the Swiss team were rewarded for their tenacity in injury-time when substitute Giovanni Sio slotted past Ciprian Tatarusanu.
Sio's goal, his first in the Champions League, means Basel trail second-placed Schalke by a solitary point with two matches remaining.
"It's not undeserved that we scored the equaliser since the second half was often one-way football. We will take the positives from this game," said Yakin.
"We fought really well and showed a lot of morale. Our chances to progress from this group are still there."
Basel's next group match is at home against leaders Chelsea on November 26.
