They understood Sunday afternoon to be on the third day since the crucifixion. But if the crucifixion had been on a Wednesday, Sunday afternoon would have been on the fourth or the fifth day, depending on how one counts. Verse 56 refers to the weekly Sabbath, and that is how Theophilus would have understood verse 54, too, since there is no hint in Luke that there may have been more than one Sabbath that week. The evidence from the book of Luke seems to point consistently to a Friday crucifixion, and Sunday is the third day from Friday. That is the way Theophilus would have counted it with the evidence available to him.
Jewish custom is to count inclusively, that is, counting the beginning as first.
In this customary way of counting days, Sunday would be considered the third day from Friday. Luke tells us that Jesus rose on the third day after the crucifixion. Another example of inclusive counting is seen in the book of Esther. Apparently any portion of the day was sufficient to count for the day and the night. A biblical phrase that seems to us to be precise may not necessarily match modern ideas of exact time measurement.