Root shared a 106-run partnership with Jonny Bairstow, who was standing in for injured wicketkeeper Matt Prior and fell just two run short of his half century before the tourists were bowled out for 418.
England's bowlers initially struggled to impose themselves on the Invitational XI, who had reached 153 for four by close of play for a lead of 39 after their first innings 304.
Root looks set to drop down the batting order to number six at the Gabba to allow Michael Carberry to come in and take his place as an opener with captain Alastair Cook.
The 22-year-old had made a sprightly unbeaten 26 on Thursday and continued in the same vein on Friday morning despite a glancing blow to his right hand from a Josh Lalor delivery which clearly stung his little finger.
After five minutes with medical staff, though, he continued his innings and his partnership with Bairstow lasted through the lunch break until the wicketkeeper was caught behind for 48.
Root stayed around through Stuart Broad's 16-run cameo before being bowled by Nic Bills after hitting nine fours in a 109-ball innings.
Carberry, who made four, was the only top six England batsmen not to get a start in the match, which will be pleasing for the tourists after their previous outing in Hobart was heavily disrupted by rain.
Light showers stopped play for just under an hour on Friday and more wet weather is forecast for Saturday's final day.
England would like a first win of the tour before they head off to Brisbane but their bowlers failed to make an impact early in the Invitational XI's seconds innings.
Aaron Finch batted at a fraction under a run a ball for his 59 and there were 81 runs on the board when he was caught by Carberry off spinner Graeme Swann.
Broad bowled former test opener Ed Cowan for 42 before Steve Finn, who took five wickets in the first innings but finished with figures of 1-53 on Friday, and his fellow seamer Boyd Rankin took the other wickets.
Prior, who has a calf strain, will undergo a fitness test on Tuesday to determine if he will be fit to play when the first test starts in Brisbane on Thursday.
- Sports & Recreation
- Michael Carberry
- Jonny Bairstow