System and method for providing fault tolerance in virtualized computer systems use a first guest and a second guest running on virtualization software to produce outputs, which are produced when a workload is executed on the first and second guests. An output of the second guest is compared with an output of the first guest to determine if there is an output match. If there is no output match, the first guest is paused and a resynchronization of the second guest is executed to restore a checkpointed state of the first guest on the second guest. After the resynchronization of the second guest, the paused first guest is caused to resume operation.