Both teams made two changes, with Glamorgan recalling strike bowler Van der Gugten and giving tall 24-year-old Australian paceman Connor O'Riordan, formerly with New South Wales academy, another chance to push his case for a longer contract.
The county is short of seam bowling resources for the closing block of the Championship, with Ned Leonard ruled out through injury, and breakthrough teenager Tom Norton also unlikely to appear again this year- highlighting the need to sign an experienced overseas bowler.
Meanwhile Essex had the luxury of resting paceman Jamie Porter, with Zaman Akhter and Charlie Bennett replacing Porter and Mitch Killeen.
Openers Thain and Benkenstein quickly tucked into all the Glamorgan bowling with the exception of Van der Gugten.
Thain was dropped off Romano Franco on 41 while Benkenstein smashed the young spinner out of the ground as the hundred came up in the 17th over.
Essex had 166 on the board by the halfway break, although Thain fell two balls later as he drilled Douthwaite to cover, having hit nine fours and a six.
Captain Tom Westley lofted Franco to long-on but Benkenstein moved confidently to three figures off just 94 balls for his maiden county century in any format.
With Benkenstein going even harder at the bowling in a stand of 67 with Matt Critchley (28), Essex looked in complete control before Glamorgan eventually found some relief.
Critchley was run out by Zain Ul Hassan in a mix-up, Benkenstein eventually chipped Douthwaite to mid-off and O'Riordan claimed his first county wicket when Grant Roelofson edged behind.
The crash of wickets continued with the last eight falling for just 55 runs, a remarkable contrast to the early Essex onslaught.
The bowlers' domination continued in the Glamorgan innings as Eddie Byrom lofted Snater to square leg and Ul Hassan (13) pulled Charlie Bennett to Jones at mid-on.
Jones was given catching practice with Colin Ingram and Jack Hope-Bell falling to mistimed attacking shots as Bennett and Snater made more inroads.
Harry Wallace's first two scoring shots on home debut were sixes, a confident pull into the pavilion and a top edge over fine leg.
Wallace, the 17-year-old son of Glamorgan director of cricket Mark, hit four more boundaries in a promising knock of 39 before Jones had him caught behind to leave the hosts 78 for five.
Hard-hitting Horton, 22, looking to secure the Glamorgan wicket-keeper's role in succession to veteran Chris Cooke, again proved his batting ability with his third substantial knock in seven games.
The century stand with Van der Gugten came off 94 balls to make sure the home crowd had something to cheer in the early evening sunshine, with the Netherlands international making his first white-ball 50.
Horton lofted four sixes and added eight fours to revive faint hopes for his side before Snater returned to induce him to slice a drive to backward point.
Glamorgan only had four wickets in hand with 84 runs needed off the final 10, and Douthwaite (13) was caught at long-off off Jones.
With captain Andy Gorvin providing willing support, Van der Gugten reached three figures in the 48th over off 93 balls and 20 were needed off the final two overs.
But Van der Gugten clubbed the final ball of the penultimate over from Snater for a straight six to leave Glamorgan needing only six off the last over.
Jones held his line and length to deliver three successive dot balls to Gorvin, and Glamorgan could manage only two singles as an unlikely victory eluded them.