He ended the day unbeaten on 98, just two short of his second championship century, to propel Yorkshire to 190 for three by the close after rain had held up play until 4.00pm when only 40 overs remained.
They now trail Northamptonshire by just 63 and will be looking to build up a sizeable first-innings lead in order to press for victory.
Yorkshire resumed on 27 without loss after five overs when play finally got under way and Adam Lyth wasted no time in boosting the score by taking two boundaries off the day’s first over from David Willey.
The left-hander also struck a backfoot cover drive for four off Lee Daggett but then slashed at the next delivery and edged to wicketkeeper David Murphy for 25.
Phil Jaques helped Root raise the 50 before he played across the line at Daggett and was lbw to leave Yorkshire on 54 for two.
Root at this stage was still progressing cautiously but he had an escape on 25 when he was dropped at first slip by Andrew Hall off Willey to give the batsman his first boundary off 54 balls.
Northamptonshire’s lively 18-year-old seamer Oli Stone put in a useful spell from the Kirkstall Lane End on his championship debut.
He claimed his maiden first-class wicket as skipper Andrew Gale shuffled across his stumps and was lbw to one which kept a shade low.
At 96 for three, Yorkshire were not yet in control but their position rapidly improved with some sparkling batting by both Root and Jonny Bairstow who had been given permission by England to play in the match.
Root, who already has a century for England Lions against the West Indies under his belt this season, completed his 50 off 89 balls with three boundaries to take Yorkshire into three figures.
He then began to open up with some vintage shots, pulling and driving Daggett for fours on his return and finding the rope against Willey with a front foot pull.
Boundaries were now coming thick and fast although Root had another stroke of luck on 83 in James Middlebrook’s second over, the off-spinner pitching down the legside and Murphy failing stump the opener.
Root was on 95 with 10 fours when he faced the day’s final over from Hall and he steered his first ball for three but Bairstow was unable to give him back the strike for the chance of a century before close of play.
The fourth wicket pair had added 94 in 20 overs together, with Bairstow on 36 not out.