With Bournemouth beating Burton, the Millers must now settle for a play-off place despite Ellison’s free-kick giving them all three points.
Nick Fenton had the first chance of the game in the 17th minute but his header was saved by keeper Jake Cole.
On-loan Middlesbrough midfielder Josh Walker then rattled the post for Rotherham as they went for the jugular.
And Ellison finally broke Barnet’s resistance in the 34th minute when his free-kick from the touch line evaded everyone and flew into the net.
It was more of the same for the Millers after the break and striker Adam Le Fondre blazed over the bar from a tight angle.
Barnet finally came into the game late on with boss Ian Hendon throwing centre-half Daniel Leach up front in search of the equaliser.
Albert Adomah had an effort blocked but, despite throwing bodies forward, Barnet couldn’t ruin Andy Warrington’s clean sheet.