Double world champion Australian Jess Fox was second-fastest in 118.02, ahead of Spain's Nuria Vilarrubla in 118.89.
Jones also picked up two touches in her opening K1 run but held it together to post a 108.39sec time, just 5.20secs behind leader Mallory Franklin (Great Britain).
"I had a massive touch on gate 2 and the poles were swinging and it wasn't a really good start to the run but overall it was solid. I guess I had a pretty fast time considering that it felt a bit off the whole way down - I'm pretty happy with how the day went and looking forward to tomorrow."
Fellow Kiwis Jane Nicholas (Tauranga) and Kensa Randle finished 45th and 60th respectively in their first K1 runs, both improving in their second runs but missing the semifinals.
Finn Butcher was the only New Zealand male to progress to the semifinals, meanwhile, although he needed to break a second-run drought to do it.
Mike Dawson (Tauranga) was the fastest Kiwi in the first run of the K1 in 37th, with Callum Gilbert (Tauranga) 41st, but Butcher picked up a controversial 50sec penalty for missing a gate.
For the first time at World Cup level, however, Butcher qualified through the repechage second run, with his 98.84sec time good enough for ninth, with the top-10 joining the top-30 from the first heat. He's enjoying the Augsburg course, which reminds him of his home Kawerau River in Central Otago.
Dawson, who made the semifinal in last week's first World Cup in the Czech Republic, finished 27th in his second run and Gilbert 43rd.
Dawson will instead turn his attention to tonight's extreme slalom division, having won gold - and New Zealand's first-ever World Cup canoe slalom medal - in that event last week.
Gilbert and Patrick Washer (Tauranga) also paddled the men's C1, with neither progressing amid tough competition led by Slovenia's Benjamin Savsek.