And Flood, who featured off the bench in England's RBS 6 Nations defeat to Wales, had initially been named on the substitutes bench was ruled out, leaving his place to Billy Twelvetrees.
George Ford, who started the semi-final, had already been named to start the game ahead of the England fly-half.
Meanwhile England skipper Chris Robshaw admitted he couldn't have dreamt of such a perfect end to the season ahead of a first-ever Premiership final for Harlequins.
Robshaw led England throughout the RBS 6 Nations and will again skipper the Red Rose on their tour to South Africa.
"If someone had told me at the start of the year that this would all happen, I would have probably laughed at them," Robshaw said.
"It was very frustrating to miss out on the World Cup. You have your dark moments and your sulks.
"But you have to get back on the horse. When you come here you are not coming to a job, you are coming to do something that you love, with your mates."