Notice that the “ed” ending of “worked” doesn’t add a syllable. The “e” is silent, and the “d” is unvoiced, so sounds like a “t”. Also notice the pronunciation of “the” when it’s followed by a vowel. It’s quite different from the dictionary pronunciation.
This phrase means “It ended well”, and you would say it about something you had been worried about, like a difficult exam. My students have exams this week, but I’m sure it will work out OK in the end.