The Spanish winger latched onto Milos Veljkovic's inch-perfect pass, controlled and fired home past Raphael Spiegel on 74 minutes.
It was a fitting finale to a fascinating encounter played at a fierce pace at the Lamex Stadium.
Earlier, Daniel Akindayini opened his account at Under-21 level as we forged ahead on 38 minutes before Kieran Bywater's equaliser eight minutes into the second half.
Veljkovic captained the team and provided the experience with Tom Carroll, Ryan Fredericks and Ceballos while goalkeeper Harry Voss made his debut and Emmanuel Sonupe his first start.
It was very much a cat and mouse affair in the first half-hour as both teams played high intensity, pressing football and space was at a premium.
We zipped the ball around with purpose and Sonupe was first to break free on 10 minutes, racing to the left byline only to see his cross slip behind Akindayini, who then had a shooting chance blocked by Reece Burke.
Voss made a routine save from Blair Turgott's 25-yard drive on 22 minutes before Spiegel was tested twice in a minute, first tipping around Sonupe's shot and then getting down to touch aside Ceballos' curler.
Elliot Lee glanced Kieron Bywater's free-kick just wide on 33 minutes with the breakthrough following five minutes later.
Josh Onomah had the luxury of a yard of space and made it count, lifting a pass to Akindayini breaking through centrally. He still had plenty to do, not least to beat the advancing Spiegel to a ball skidding off the surface, but he got there first and hooked home from the left angle.
Nathan Oduwa replaced Sonupe at half-time and the second half sparked into life after West Ham's equaliser on 53 minutes as Bywater's free-kick from the left touchline found the top corner.
Akindayini missed a golden chance to restore the lead three minutes later after Carroll charged down a clearance and then Spiegel just clung onto Ceballos' cross from the left byline.
Voss made two key saves in as many minutes to deny Lee, the first down to his right from 16 yards and then the save of the night, scampering across his line to block from point-blank range as the striker slid in to meet Matthias Fanimo's cross.
We carved out a carbon-copy chance on 68 minutes as Oduwa played a one-two with Carroll and delivered from the right but Ceballos couldn't turn home at the far post.
The winner arrived on 74 minutes. Veljkovic picked up a clearance on the half-way line and picked out Ceballos' run on the right angle of the box. Ceballos controlled and lashed past Spiegel, a fine finish.
West Ham pushed for an equaliser and their best chance arrived two minutes from time as Lee broke into the box with only Dominic Ball blocking his path to goal but the defender provided a textbook block to repel the danger.
Spurs U21: Voss; Fredericks, Ball, Veljkovic (C), McQueen; Carroll, Winks; Sonupe (Oduwa, 46), Onomah (Lesniak, 69), Ceballos (Miller, 75); Akindayini. Subs: Glover (GK), Coulibaly.
West Ham U21: Spiegel, Westley, Potts (C), Poyet, Oxford, Burke, Turgott (Sadlier, 74), Cullen (J Brown, 84), Lee, Bywater, Lletget (Fanimo, 64). Subs: T Brown (GK), Page.