The series, which saw South Africa overtake England at the top of the world Test rankings, was defined by England's failure to take key wickets, and Flower has said that England's bowlers were outperformed.
"We had our chances," Flower told Cricinfo. "At Lord's we dropped two crucial catches. They've caught well in the slip area but I think their bowling attack was a little bit more incisive than ours. I don't think that's unfair on our bowlers to say that.
"Their batsmen cashed in and got the big, match-turning innings. Yes, with the assistance of a dropped catch here and there from us.
"However in the main they deserved to win. We haven't grasped the opportunities that came our way. And, against a good, hardened, experienced side like South Africa, you'll suffer the consequences of that."
England and South Africa will now play five one-day internationals, which begin this Friday, and three Twenty20 matches.