With Mike Tindall is still struggling with the dead leg he picked up in the 16-12 pool win over Scotland, Flood has got the nod ahead of Shontayne Hape at inside centre for Saturday's quarter-final.
That means a return to the second playmaker tactic Johnson previously employed before he resorted to having a strong ball carrier in the No.12 jersey.
And with Flood having played alongside fly-half Jonny Wilkinson in the past - during their time together at Newcastle and for England - Johnson has backed the pairing to shine.
"It's not a gamble. You always put a lot of thought into your selections, no more so than when you're in a World Cup quarter-final," Johnson said.
"It's one of the options we've got. I think Mike and Manu (Tuilagi) have played well together. If we had to play Shontayne; there's always an argument to play him.
"It does give us some different things that we can do on the field when we play those guys (Flood and Wilkinson).
"Mike took a couple of bangs last week and hasn't really been available to us this week.
"That was part of the equation - Mike's injury and Toby playing very well."
Johnson has also named Tom Palmer, Mark Cueto and Nick Easter in his line-up for the encounter.
And Johnson admitted the decision to go for Easter over James Haskell has been a tough call.
"I said in front of the team that it's a particularly hard call on James. He didn't deserve it in terms of how he's played," said Johnson.
"But they will have a massive influence on the game. I've said this before. The guys on the bench are normally on the field at the end.
"Everyone wants to start, we all know that, but actually your role is no less coming off the bench."
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