Duke settled things quickly by taking a 52-32 lead into halftime, and started the second half with a 16-6 run.
Thomas went 8-for-8 from the field and scored 12 first half points.
Kyle Singler compiled 17 points, seven rebounds, four assists and three steals for Duke. Nolan Smith scored 11 with three assists, while 11 of 12 players scored for the Blue Devils (7-0), who won their 64th straight home game against a non-ACC opponent.
Damian Saunders' 22 points, 10 rebounds and three assists paced outmanned Duquesne.
Aaron Jackson scored 14 with six rebounds, while three others scored seven points for the Dukes (4-1), who suffered their third straight loss at Duke's famed Cameron Indoor Stadium.