With Champions League qualification far from assured, City was unable to defeat a resilient, and relation threatened Middlesborough, with the match ending 2-2.
However, Guardiola believes the result was not an accurate reflection of the game he watched.
"We deserved to win," the Spaniard told The Daily Mail. "In the second half they crossed the halfway line twice. We were much better."
City will next face Crystal Palace at the Etihad on Saturday.