Flood, gaining his 24th cap, made his first start of the this season’s Championship and scored a 39th-minute penalty to level the scores at 3-3 before being replaced by Andy Goode in the 67th minute.
Ellis gained his 25th England cap, while clubmates Julian White and Tom Croft were used as second-half replacements.
White, who now has 47 caps, appeared as a front-row replacement while former England skipper Phil Vickery was in the sin bin and returned to the field when Andrew Sheridan was withdrawn during the closing stages. Croft, gaining his 11th cap, was a 70th-minute replacement for Joe Worsley.
Hooker George Chuter travelled to Dublin with the England squad but was not called into the matchday 22 as Dylan Hartley confirmed his fitness and was included among the replacements.
Geordan Murphy was unused on the Ireland bench as Declan Kidney’s squad made it three wins from three and kept alive hopes of a Grand Slam.
Benjamin Kayser came off the bench in the 65th minute as France ended Welsh dreams of a Grand Slam on Friday evening.
The French came from 13-3 down to win 21-16 at the Stade de France, with Kayser collecting an eighth international cap.
Martin Castrogiovanni gained a 56th cap for Italy as they were beaten 26-6 by Scotland at Murrayfield.
A try from Tigers Academy wing Will Hurrell was not enough for England Under-20s as they lost their unbeaten run in the age-group championship.
England were beaten 19-18 by Ireland in Athlone, with the hosts claiming a late drop goal to snatch victory.
Hurrell was joined in the starting XV by Tigers full-back Greig Tonks, while scrum-half Sam Harrison claimed a first cap as a second-half replacement.