It looked like the Blues would have to settle for a draw when Cesar Azpilicueta was controversially judged to have fouled Valentin Stocker in the box, and Fabian Schar dispatched the penalty.
|EUROPA TROPHY FOR THE BLUES?|
|8/13||Chelsea are 8/13 with Bet365 to win the Europa League this season|
"We had enough chances to score an away goal, but the penalty was a surprise for everyone and that could have made a difference," Benitez told reporters.
"I couldn't see why it was a penalty. The ball was in the air and it was a very, very strange decision.
"We know [Basel] is a very good team, who can score goals home and away, so we have to be sure to concentrate.
"We can't be over confident in the next game but we know that, if we play well, we can beat anyone."
The Blues will be without suspended full-back Ashley Cole after the England international picked up a booking for time-wasting, meaning he will miss the return leg at Stamford Bridge.