The 37-year-old former Titans seamer removed Sussex trio James Anyon, Rory Hamilton-Brown and Ed Joyce for a hat-trick before bowling Matt Machan with the first delivery of his next over.
He finished with figures of 5-40.
Sussex crumbled from 33-0 to 33-5 in 10 balls and were all out for 178.
Somerset scored 107-4 to seal victory with a day to spare, as they climbed to the top of Division One.
The last player to take four wickets in successive balls during an English Championship match was Gary Butcher while Thomas is the first man to achieve it in any first-class cricket since 2011, when Neil Wagner did it for Otago against Wellington.
The last South African to take four in four was Charl Willoughby who achieved the feat in a first-class match for Cape Cobras against the Dolphins in Durban during the 2005-06 season.
