In Game 3 of the ALCS against the White Sox, Flanagan held the team to one run before getting replaced by Sammy Stewart in the sixth inning with his team up 6–1. He was awarded the victory in the 11–1 triumph, and Baltimore went on to defeat Chicago in four games. He started Game 3 of the World Series against the Philadelphia Phillies, giving up solo home runs to Gary Matthews and Joe Morgan before getting pinch-hit for by Ken Singleton in the fifth inning, as Baltimore had a man on second with two outs and a chance to score its first run against Steve Carlton. Singleton struck out, but the Orioles went on to win 3–2 before eventually winning the series in five games. Though 1979 was his best season statistically, Flanagan considered the World Championship campaign of 1983 as his best year in baseball.