David Luiz was the hero at St Jakob Park, scoring a driven free-kick with what was the last kick of an intense first leg.
Victor Moses had put the Blues ahead after 13 minutes but they were unable to add another - and their evening worsened three minutes from time when referee Pavel Kralovec awarded a soft penalty against Cesar Azpilicueta, allowing Fabian Schar to slot home the equaliser.
"All around me nobody felt that it was a penalty because the ball was in the air, it was a very strange decision," Benitez said.
"I was a little bit worried about this penalty. For us, it wasn't [a penalty]. To give a penalty it has to be very, very clear."
Clearly aggrieved, Chelsea returned to the attack with renewed vigour and eked out a winner to put them in the driving seat ahead of next week's return leg at Stamford Bridge.
"I think it's true that we had this feeling that we didn't deserve to concede this goal, which was an extra motivation," he added.
"We had chances on the counter-attack and we couldn't score a second goal, but yes [the 2-1 win was deserved]. I think we had to work hard until the end.
"It is always important to win. To score an away goal is important but to score two and win is even better. David Luiz did a great job but I am really pleased for the team because they all did well.”