The Saints played their final tune-up before taking part in the first game of the NFL's regular season next Thursday night against Super Bowl champion Indianapolis.
Thomas, a rookie, ran for 81 yards and caught two passes for 47 more, as the Saints finished their exhibition campaign at 3-2. The regular starters for both teams saw limited action.
New Orleans backup quarterback Jamie Martin completed 11 of 15 passes for 136 yards.
Miami's John Beck was good on eight of 15 passes but was intercepted twice.
The Dolphins (2-2) open on the road against Washington.