Flood, who came on at centre as a second-half replacement, converted Ben Morgan’s 77th-minute try to take his international total to 301 points.
The Leicester Tigers fly-half is fourth on England’s all-time scoring list behind Jonny Wilkinson (1179 points), Paul Grayson (400) and Rob Andrew (396).
England scored four tries in during Saturday’s Test. Joe Launchbury, Billy Twelvetrees and Chris Ashton crossed the whitewash in the first-half before Morgan’s late score. Owen Farrell landed three conversions and five penalties.
England complete their autumn international series against New Zealand at Twickenham on Saturday.