Both players were on the floor when Thomas pushed her fist into Clark's throat before getting up and stepping over her.
Germany finish top of Group E, with Ivory Coast second and Ecuador will have a chance of qualifying on third place.
The West Africans will face the second-place finisher between France and Norway in Group I on Tuesday in Texas.
Shafali Verma's half-century helps the 50-over world champions reach the target inside 17 overs at Old Trafford.