The Bundesliga side's coach was angry at the physical nature of the Spaniards' play on Tuesday, but sporting director Rudi Voller vowed to celebrate in style.
Omer Toprak's solitary strike was enough to secure a place in the knockout phase for the Bundesliga side.
However, Hyypia felt the referee should have intervened over a number of heavy challenges from the hosts.
"I was angry that the referee didn't show any red cards after the harsh fouls of Sociedad," he said after the match. "But the referee decides. I can't understand why Sociedad would do something like this in a match like that. They were eliminated anyway."
Leverkusen's win was enough to secure their place in the next round behind Manchester United, who beat Shakhtar Donetsk 1-0 at Old Trafford.
And Hyypia was pleased with his side's response to its 5-0 thrashing at the hands of the Red Devils on matchday five.
"The team showed character," he added. "First I thought we were tired but then we made our game. I said at the break that we would at least score one goal from a set piece."
Sporting director Rudi Voller revealed he plans to celebrate his side's progression in style after what he felt was a fully-deserved win.
He added: "We entered this game with a lot of confidence and knew that we would have a chance to win and in the end deserved the victory. I'll be having a cigar and a glass of red wine to celebrate."