The Ivorian was involved in putting the visitors in the lead as he broke forward and supplied an assist for Edin Dzeko, while Aleksandar Kolarov restored City's advantage in the 85th minute after a deflected Marcelo strike had cancelled out the Bosnian striker's finish.
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The former Barcelona man told reporters after the game: "It was a pity, because we had the victory very close and we lost it with two goals in the last two minutes. Let's see what we can do next game, which will be very important for us."
Toure went on to praise City's opponents on the night, hailing their determination as well as the home support and Jose Mourinho, who he labelled as "great".
He added: "Real Madrid is always Real Madrid. They really wanted to win, with the support of their fans.
"They have a great team, with a great coach."