You can use the securityContext in Deployment in the same way you use it inside Pod.
Like it was already suggested by placing it under template.spec:
apiVersion: apps/v1
kind: Deployment
metadata:
  name: test-deployment
  labels:
    app: test
spec:
  replicas: 3
  selector:
    matchLabels:
      app: test
  template:
    metadata:
      labels:
        app: test
    spec:
      securityContext:
          runAsUser: 2000
          runAsGroup: 3000
          fsGroup: 2000
      containers:
      - name: test
        image: busybox
        ports:
        - containerPort: 80
        command: [ "sh", "-c", "sleep 1h" ]
And you can test it:
$ kubectl exec -it test-deployment-54d954d7f-2b582  sh
/ $ ps
PID   USER     TIME  COMMAND
    1 2000      0:00 sleep 1h
    6 2000      0:00 sh
   11 2000      0:00 ps
/ $ whoami
whoami: unknown uid 200