The hosts scored a late equaliser through Fabian Schar, but Chelsea battled back to score a last-gasp free kick.
Sommer said that the defeat to a team that he thought was no better on the night was a harsh result to take for Basel.
"In the end, we can take many a positive thing from the game despite the 1-2 scoreline," he told UEFA.com. "I think that we were the better team but we made too many unforced, individual errors.
"We could have scored more goals than we managed and the second Chelsea goal was unlucky for us.
"This goal is a slap in the face for us because we did a lot, we ran a lot, we tried a lot and then we give away a goal like that in the last minute. I don't think they were the better team but they won and this is the only thing that counts."
The return leg takes place next Thursday night.