The result is enough to move the Warriors into third place in the RaboDirect PRO12 while their visitors on the night drop to eighth in the table.
Both sides came into the game looking to bounce back from disappointing Heineken Cup defeats last week having begun with home wins.
Glasgow slumped to a big defeat to reigning champions Leinster after their last-gasp victory over Bath while Ulster failed to follow up an impressive home win against Clermont against Leicester at Welford Road.
And it was the home side who moved into an early lead as Duncan Weir kicked a penalty from wide on the right after Simon Danielli had been penalised for holding on.
Humphreys brought his side back into it with a penalty but a high tackle from Adam Kyriacou was penalised to give Weir the chance to give Glasgow back the lead which he duly took to make it 6-3.
Weir added another penalty from the right to extend the lead but after David Lemi failed to release Adam D'Arcy, Humphreys had the opportunity to get Ulster back into it. However his penalty attempt went well wide to give Glasgow a 9-3 half-time lead.
Ulster came out the quicker in the second half and Humphreys went some way to make amends for his earlier miss with a penalty to bring the visitors back to within three points.
He again held his nerve 15 minutes into the second half as he slotted another penalty from the right to draw Ulster level at 9-9.
Ulster piled on the pressure but struggled to take advantage with Humphreys missing two more kickable penalties as he struggled to recreate the form he showed against Clermont and Leicester.
And Glasgow made him pay as former Connacht centre Nathan crossed after an unexpected turnover.
Nathan collected the ball out wide before slipping it to debutant winger David Lemi who fed back inside to his centre to cross and make it 14-9, Weir just missing a tricky conversion attempt.
And having brilliantly got themselves into position, Henry Pyrgos found Weir who slotted the drop goal from in front to make it 17-9 and guarantee the win.
|Glasgow Warriors Score Card|
|Ulster Rugby Score Card|