The White Rose’s third Specsavers County Championship victory in eight matches also deepened their arch-rivals relegation worries given they have only secured one win from their first nine outings, losing five.
Steve Patterson’s side were defending a target of 323 and started day three on the verge of a 19-point haul.
Lancashire, who claimed only two points having been deducted one for a slow over-rate, were 194 for six with only Tom Bailey, unbeaten on 38, Graham Onions, Jimmy Anderson, Matthew Parkinson and injured Liam Livingstone to bat as they pursued another 129 runs to win.
Home captain Livingstone fractured his left thumb whilst fielding on day one, did not bat in the first innings and came out number eleven in the second without facing a ball as Lancashire lost their last four wickets for 10 runs.
He now faces a significant spell on the sidelines.
Root, having dismissed Jos Buttler in the penultimate over of day three, struck with the first ball of day three when Graham Onions edged behind for a duck (194 for seven in the 49th).
Then, shortly afterwards, he had Matthew Parkinson caught at first slip as the score fell to 196 for eight in the 53rd and later bowled Anderson on the way to career best figures of four for five in 204 all out. Steve Patterson also trapped Tom Bailey lbw.
Yorkshire started this match second-bottom in the table, three points behind Lancashire with a game in hand.
They are now 14 points clear of the Red Rose with that game in hand still in tact.
They have also jumped over Hampshire, who have not played this round and are in the relegation zone as a result.
Hampshire are one point behind Lancashire with a game in hand and 15 points behind Yorkshire with both counties having played eight.
Only five batsmen posted half-centuries in this bowler-friendly fixture, with Jonny Bairstow’s second-innings 82 the best of them.
Lancashire have not won a Roses Championship match since completing the double in 2011, the year they won the title and Yorkshire were relegated.
Since then, Yorkshire have won four meetings at home and away and drawn three.
Attentions now return to the Vitality Blast, with Lancashire leading the North Group with five wins from six and Yorkshire having won three from five.
Their next Championship outings come late next month (August 19).
Lancashire travel to the Oval to face leaders Surrey in a pink ball fixture, while Yorkshire host bottom side Worcestershire at Scarborough.
The Red Rose have only got one more home match in their remaining five - against Worcestershire at Southport - as the Old Trafford outfield gets relayed ahead of a busy 2019 summer.