An example method is described to provide fault tolerance in a virtualized computing environment with a first fault domain and a second fault domain. The method may comprise determining whether a first primary virtualized computing instance and a first secondary virtualized computing instance are both in the first fault domain. The method may comprise: in response to determination that the first primary virtualized computing instance and first secondary virtualized computing instance are both in the first fault domain, selecting a second secondary virtualized computing instance from the second fault domain; migrating the first secondary virtualized computing instance from a first host to a second host; and migrating the second secondary virtualized computing instance from the second host to the first host, thereby swapping the first secondary virtualized computing instance in the first fault domain with the second secondary virtualized computing instance in the second fault domain.