Warnapura was unbeaten on 149 in a total of 426, but a target of 87 was too easy for North, who won in 18.1 overs with Aakash Chopra backing his first-innings hundred with an unbeaten 51.
North remain the most successful team in the history of Duleep Trophy and had last won the tournament in 2003-04 in Mohali.
The victory today was inevitable once Sri Lanka 'A' lost the plot in their first innings being skittled out for a paltry 296 on a batting paradise.
North piled on their agony posting a Herculean total of 636.
With a 300 plus run deficit on their shoulders it was impossible to save the match and the inevitable happened. They lost the first four wickets yesterday and began 81 runs behind today, and lost four wickets in the first session.
Chamara Silva, Kaushal Silva and Rangana Herath all got quick starts but were done in by their flamboyant strokeplay and sometimes the lack of it. At the other end was Warnapura, all resolve or skill. Overnight on 82, Warnapura was cautious while in the nineties, but brought up his hundred with a four off Ashish Nehra and collected three more in the bowler's next.
Warnapura battled on amid a ruin of wickets as Sri Lanka 'A' raced towards their doom.
Rajesh Sharma, the off-spinner from Punjab, picked two more to finish with season's second first-class five-wicket haul. Nehra, who looked rusty and out of sorts, got the wickets of Kaushal and Herath, while Mithun Manhas got one to ensure an Indian victory.
North reached the target of 87 losing Ricky and Gambhir, but an undefeated 51 from Akash Chopra meant that North were unstoppable.