Toure side-footed home from six yards in the 43rd minute for Barcelona, which lifted the Champions League title for the second time in 2006.
"After the first leg result, they had nothing to lose and were out to spring a surprise," said Barcelona coach Frank Rijkaard. "They were playing well and I think that made us a bit nervous as we tried to wrap things up."
Toure's goal was set up by 17-year-old striker Bojan Krkic, who had scored Barca's scorer in the first leg. He flew down the right wing before serving up Toure.
In La Liga play, Barcelona has won just once in its last six games.
Both Schalke and Barcelona squandered several chances.
Among those blowing opportunities was Barcelona's Thierry Henry, who was booed by the Camp Nou fans.
Argentine Lionel Messi may return from a thigh injury in time to replace Henry in the first leg against Manchester United April 23 at the Camp Nou.