The 24th-ranked Thiem added the Swiss trophy to the Croatia Open he won one week earlier. Thiem's run of three clay-court titles this season started in April at Nice, France.
In a match of nine service breaks, 14th-ranked Goffin won four straight games in the first set and served with a 5-4 lead.
Thiem leveled when Goffin double-faulted and broke again to clinch the set.
The third-seeded Thiem dropped serve to open the second set but lost only more game in closing out the match in a little under 90 minutes.
Thiem is top-seeded next week in another clay-court event, at Kitzbuehel in his native Austria.