David Luiz was the hero of the semi-final at St Jakob Park, scoring a driven free-kick with what was the last kick of an intense first leg.
Asked if the 2-1 win was deserved, Benitez said: "Yes, I think we had to work hard until the end. I think we had chances on the counter-attack and we couldn't score a second goal."
Victor Moses had put the Blues ahead after 13 minutes but they were unable to add another in regulation time, with wayward finishing, fine goalkeeping and plain bad luck thwarting them.
Chelsea's 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. 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.
Benitez added: "After the penalty, which was a surprise for everyone, I think in the end the second goal from David Luiz was good enough for us. But 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."
Having seen London rivals Tottenham exit to Basle in the quarter-finals, Chelsea were well aware of the threat posed by the Swiss champions.
"We have the experience from Tottenham so we know this team is a very good team who can score goals home and away, so we have to be sure to concentrate," the Spaniard said. "We can't be over confident in the next game and do our job. We know that, if we play well, we can beat anyone so we can do it."
Benitez's Basle counterpart Murat Yakin cut a forlorn figure in the post-match press conference.
"My team tried to dominate the match and be creative all the way through," the former Switzerland international said. "We were well organised but so were Chelsea and set up well, especially defensively. We just didn't find the free spaces."
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