The South Africa batsman, resuming on 66 not out, finished unbeaten on 101 as Sussex took just over an hour to finish off the formalities.
A 112 stand between Van Zyl and Laurie Evans (51) looked set to lead Sussex to victory but the latter fell to Matthew Salisbury with just one run required.
Stiaan van Zyl scored an unbeaten century to guide Sussex to their first Specsavers County Championship victory of the season.
The finished the job this morning, defeating Durham by six wickets at Emirates Riverside with Van Zyl still there on 101 from 149 balls.
Beginning the final day on 144-3, the visitors still had a challenge to score the 68 runs that would carry them over the line on a gloomy morning.
Laurie Evans offered a chance in the morning session when he drilled a Chris Rushworth delivery straight to Jack Burnham at cover – but he put the chance down.