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The Bayern Munich coach has signed a three-year contract to succeed Manuel Pellegrini this summer.
Sunday's defeat by Manchester United has put City's top-four place in doubt, leading to discussion over whether Guardiola has an escape clause.
But BBC Sport has learned no break clause exists, so the 45-year-old Spaniard will join in July as planned.
Sunday's defeat means City are in the fourth and final Champions League qualifying slot, a point above West Ham and Manchester United.
All three teams have played 30 Premier League games.
Former Barcelona boss Guardiola has never coached in the Europa League.
Pep Guardiola will be Manchester City manager next season even if the club do not qualify for the Champions League.