The winger opened the scoring in the sixth minute before a quickfire double took the game beyond Southampton's reach in the second half.
Jon Obika was also on target as a young team - including debutants Tom Gardiner, who started at centre-half and substitute Victor Zapata-Caicedo, both Second Year Academy trainees - dominated at the Saints' Staplewood training complex.
Ceballos handed the team the perfect start by drilling home from the edge of the box in the sixth minute and it was 2-0 two minutes later as Obika was in the right place to finish after Yago Falque's shot cannoned back off the crossbar.
Falque, Ceballos, Obika and Grant Hall all had chances but the home side registered next as Sam Hoskins finished one-on-one to make it 2-1 just before half-time.
Ceballos restored our two-goal advantage with another sweet strike from 18 yards 10 minutes into the second half and claimed his hat-trick in the 62nd minute, a tap-in from Falque's square pass.
The teams shared chances after that as Tom Carroll and substitute Nabil Bentaleb went close while at the other end, Vigouroux denied Hoskins and Ben Reeves.
Will Britt produced a fine save to keep out Carroll and Zapata-Caicedo headed wide before Southampton had the last word as Calum Chambers struck in injury time for 4-2.
Spurs Under-21s: Vigouroux, Barthram, Stewart, Gardiner, Hall, Carroll, Falque, Parrett, Obika (Zapata-Caicedo, 75), Pritchard (Bentaleb, 71), Ceballos (Munns, 75). Unused sub: Miles.