The summer signing's spot kick was enough to see off the Highwaymen at the Towbar Express Stadium @ The Turnbull Ground, with Nathan Haslam's men coming out on top in a well contested cup tie in front of their own supporters, writes Liam Ryder.
The win - Whitby's third in four games - keeps their hopes in the competition well and truly alive as Town look to reach the First Round Proper for the first time in 20 years.
An end-to-end first half brought several attempts on goal for both sides, with some of those being huge chances that perhaps should have found the back of the net.
Alfie Doherty forced Daniel Lowson into a comfortable save early one as Whitby looked to get on the front foot straight from the kick-off.
Gratton looked for an opener for the Seasiders, but he would be denied by Lowson from a tight angle ahead of Jeff Henderson's clearance behind for a corner, before Morpeth had their first opening which resulted in Jack Foalle firing an effort over the crossbar from range.
Andrew Johnson saw a curling strike saved by Shane Bland and then his opposite number, Lowson, almost gifted Whitby the first goal of the afternoon as his ball out from the back was intercepted by Gratton. Lowson would make amends, tipping the midfielder's effort from distance around the post.
Perhaps the clearest opening of the first half fell to Whitby in the 14th minute. Lowson's spill following a Junior Mondal free-kick saw the ball fall to Lewis Hawkins, but he could only drill his powerful strike high over the bar, as the visiting 'keeper was let off for a second time.
Despite an initially serious looking shoulder injury to Daniel Rowe just before half time, the Whitby captain remained on the pitch for the second half and within minutes of the re-start, Haslam's men made their second half intent known as they began on the front foot.
Four minutes after the resumption of the match, Mondal had a great chance to give his side the lead when his initial free-kick was straight into the wall, but, on the rebound, he fired in a thunderous strike which was well held by Lowson.
On the hour mark, Whitby had the lead; Gratton fed Mondal, who got goal side of Henderson before going to ground which resulted in the Seasiders being awarded with a penalty kick.
Gratton, who converted twice from 12 yards in the midweek NPL premier division victory over Marske United, stepped up to drill the ball low past Lowson into the bottom corner.
Only a timely block from Liam Miller prevented Whitby from doubling their lead shortly after when Mondal squared the ball to substitute Jerome Greaves as Haslam's men looked for another.
Whitby's opponents from Northumberland, created their own chances but were either denied by the outstanding Bland, or the resolute Whitby defence as they threw everything they had at the home side.
But the Blues remained a threat on the counter attack with Priestley Griffiths, Doherty and Soni Fergus all having chances to kill the cup tie off.
The final exchanges remained nervy however following on from Whitby's failure to capitalise on the openings they were presented with, giving Morpeth that extra bit of confidence to snatch a draw and force a replay.
It wasn't to be for the Highwaymen, though, and it was Whitby who booked their place in the final qualifying round of the competition.