Her compatriot, Olympic gold medallist Peter Thomsen, was second on Parko 4 and, following this fifth leg of the World Cup, the two German riders have qualified for the Final at Strzegom, Poland, in August.
Marina Kohncke and Calma Schelly won the Malmo World Cup qualifier at the weekend. © Lotta Gyllensten/FEI
This allowed Karin Donckers (BEL) and Lamicell Charizard to move into second, but 12 faults in the jumping relegated them back to fourth, behind Peter Thomsen (GER) and the upward-moving Finn, Sanna Kiltakorpi.
Kohncke had two jumping fences in hand to win and when she hit the fourth, the audience held their breath, but she kept her dark bay Holsteiner mare balanced for three time penalties and victory was hers.
"This is only my second 3* start on Calma Schelly," said Kohncke, "so I'm really pleased with the way she performed. I don't know yet about the Final; I shall see how it goes."
Sanna Kiltakorpi (FIN) rose from 12th after dressage to eventual third on Lucky Accord, having completed the fastest cross country (5.6 penalties) and produced the only clear jumping round.
Kiltakorpi, 22, represented Finland at the 2007 FEI Young Rider European Championships. The 10-year-old Lucky Accord, a Swedish warmblood by Acacio, has already won at 1* and 2* level.
HSBC FEI World Cup Eventing Rankings (after 4 out of 9 qualifiers)
1 Megan Jones (AUS) 142 points
2= Simone Deitermann (GER) 71
2= Marina Kohncke (GER) 71
4= Heelan Tompkins (NZL) 67
4= Georgia Clifford (AUS) 67
4= Julia Mestern (GER) 67
4 = Peter Thomsen (GER) 67
8= Matthew Grayling (NZL) 64
8= Stuart Tinney (AUS) 64
8= Michael Jung (GER) 64
11 Tim Lips (NED) 61
12 Kai Ruder (GER) 58