The 25-year-old Garmin Sharp rider won the 190.3km stage in 4 hours, 51 minutes, 49 seconds.
Enrico Gasparotto of Italy was second for the Astana team, and Wednesday's stage winner, Gianni Meersman of Belgium, was third for Omega Pharma-Quick Step.
Froome retained the lead he has held throughout the six-day race through French-speaking Switzerland, which ends on Sunday. Another Garmin rider, Andrew Talansky of the United States, trails Froome by six seconds.
Friday's stage covers 181km, starting and finishing in Payerne with some lower category climbs.
Results on Thursday from the third day of the Tour of Romandie, a 190km stage from Prilly to Granges:
1. Ramunas Navardauskas, Lithuania, Garmin-Sharp, 4 hours, 51 minutes, 49 seconds.
2. Enrico Gasparotto, Italy, Astana, same time.
3. Gianni Meersman, Belgium, Omega Pharma-Quick Step, same time.
4. Luka Mezgec, Slovenia, Argos-Shimano, same time.
5. Dominik Nerz, Germany, BMC Racing, same time.
6. Francesco Gavazzi, Italy, Astana, same time.
7. Jan Bakelants, Belgium, RadioShack Leopard, same time.
8. Stef Clement, Netherlands, Blanco, same time.
9. Michael Albasini, Switzerland, Orica-Green Edge, same time.
10. Manuele Mori, Italy, Lampre-Merida, same time.
Overall standings (After 3 of 6 stages):
1. Chris Froome, Britain, Sky, 9 hours, 34 minutes, 13 seconds.
2. Andrew Talansky, United States, Garmin Sharp, 6 seconds behind.
3. Robert Kiserlovski, Croatia, RadioShack Leopard, 0:13.
4. Richie Porte, Australia, Sky, 0:15.
5. Rui Costa, Portugal, Movistar, 0:16.
6. Thibaut Pinot, France, Francaise des Jeux, 0:17.
7. Stef Clement, Netherlands, Blanco, same time.
8. Alejandro Valverde, Spain, Movistar, same time.
9. Tom Danielson, United States, Garmin Sharp, same time.
10. Wilco Kelderman, Netherlands, Blanco, 0:18.