Sagan, who also won the first stage, finished ahead of Belgium's Edwards Theuns and Rudy Barbier of France.
Thursday's fourth stage is over 154.2km from Riemst to Lanaken.
3rd stage results
1. Peter Sagan (SVK/Bora-Hansgrohe) 4hr 14:01, 2. Edward Theuns (BEL), 3. Rudy Barbier (FRA), 4. Dylan Groenewegen (NED), 5. Loïc Vliegen (BEL) all same time
Overall standings
1. Stefan Küng (SUI/BMC) 8hr 15:08, 2. Maciej Bodnar (POL) at 04, 3. Tom Dumoulin (NED) 05, 4. Peter Sagan (SVK) 05, 5. Søren Kragh Andersen (DEN) 08