The Seasiders conceded twice in the first-half at Nethermoor Park, with Jameel Ible's close-range header opening the scoring inside the first 20 minutes before Will Longbottom's strike doubled the hosts' advantage.
Adam Gell pulled a goal back for Town just past the half-hour mark, netting his second goal since returning to the club from Bishop Auckland, before Longbottom's second-half strike confirmed defeat in West Yorkshire for Gary Liddle's side.
Aiming to move into the top ten of the Pitching In Northern Premier League Premier Division with a victory against the Lions, Liddle made one enforced change to the side which claimed a 3-0 win against Lancaster City the previous Saturday as Connor Smith was handed a start in place of the injured Jassem Sukar at a blustery Nethermoor Park.
Layton Watts came close to firing Town into an early lead as the recent arrival from West Auckland Town's powerful shot was acrobatically saved by Joe Cracknell.
Whitby suffered further disappointment in the 17th minute as their former defender Ible netted for the hosts, with the St Kitts & Nevis centre-back, deployed at left-back for the afternoon, heading home from Longbottom's left-wing corner.
Town could have fallen behind prior to this as Longbottom struck a free-kick from distance on target but safely into the hands of Shane Bland.
In the 26th minute, though, Guiseley extended their lead through Longbottom, who picked up Jack Emmett's pass just outside the box before quickly driving a high effort past Bland and into the top left-hand corner.
Whitby pulled a goal back with ten minutes to play of the first-half through Gell. The midfielder held the ball well on the edge of the 18-yard box before calmly slotting the ball into the bottom left-hand corner of Cracknell's goal.
Bland prevented Longbottom from adding his second with a similar save to the one he produced earlier on the half, once again getting right behind the league's top scorer's set-piece.
Cracknell recorded a strong save to deny Connor Simpson from equalising, blocking the striker's powerful effort from distance after he had driven forwards towards goal.
The Seasiders continued their pursuit for an equaliser without creating anything too clear cut but their hopes were shattered when they got caught by a swift counter-attack from the hosts.
In the 73rd minute, Whitby's hopes of avoiding defeat were distinguished as Longbottom netted Guiseley's third goal of the afternoon. The ball was intercepted in midfield before the Lions broke with pace. Frankie Whelan looked to have done enough to regain possession for Town, but he lost his footing, allowing Longbottom to strike into the bottom corner.
Sam Collins denied Longbottom from getting Guiseley's fourth goal of the afternoon after the winger dangerously found space to strike inside the area before his strike towards the far post was bravely blocked by the foot of the Seasiders defender.