Thomas racked up 212 yards on 15-of-23 passing for the Hokies (2-0), who posted a one-sided victory after barely eking out a win in last week's overtime triumph over Georgia Tech.
Corey Fuller made two catches, for 44 yards and a touchdown.
Jake Ryan could manage just 8-of-21 through the air for 62 yards and two interceptions for the Governors (0-2).
Wesley Kitts rushed for 110 yards on 22 carries.
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