Sagan managed to outstrip Baden Cooke with just 50m to go as he stormed to the finish line.
Saturday's winner against the clock continued his fine form as he surged to victory ahead of Cook and Team Sky's Ben Swift.
Portugal's Rui Alberto Faria Da Costa holds the overall lead after a string of consistent displays.
The 194.7km stage began in Martigny and ended in Aarberg.
Tuesday's stage four will see the riders negotiate the 189km from Aarberg to Trimbach.