The elite women's event provided an exciting field, with stiff competition from the likes of Olympians Razarenova and Ukrainian Yuliya Yelistratova.
Both Razarenova and Yelistratova are in their first full season after giving birth last year, with Yelistrova dominating the European rankings this season.
Until just an hour before the race it was unclear whether the athletes would be facing a triathlon or a duathlon, due to concern over contaminants in the water.
The choppy conditions proved a challenge, particularly for Thomas who was one of the last out after getting caught in a scuffle during the swim.
The cycle course was tough, incorporating a long, steep climb as well as some challenging technical points to really test the athletes.
Razarenova managed to stay in the lead group for the cycle, gaining 15 seconds on Yelistratova, while Thomas posted the eighth fastest time in the bike, making up for the disappointment of the swim.
However, it was during the run that Yelistratova and Razarenova really showed their class, delivering the fastest two times in the field.
Yelistratova's incredible 16.12 5km run brought her up to third position, but she was unable to catch Lena Meißner who took second place behind Razarenova.
Thomas put in a respectable run but struggled to keep pace after her impressive bike performance.
"The bike took a lot out of my legs and then I just didn't have it on the run," she admitted. "That's not what I came here for, but it is what it is."
While the gold medal went to Razarenova, the overall European Cup title went to Yelistratova who has won every year since 2014, apart from her break last season.