Kazakhstan's Lutsenko took the honours over the 152.5-kilometre stage in and around Bern.
Belgium's Jan Bakelants, of AG2R, and France's Warren Barguil of the Giant team came in second and third respectively.
“This is the biggest win of my career,” said Lutsenko, a former under-23 world champion.
“I paced my attack 20 kilometres from the finish. I wasn't too worried about Bakelants as I knew I could beat him in a sprint.”
Pinot again lost time in the overall standings as closest rival Geraint Thomas of the Sky team chipped three seconds off the Frenchman's lead.
He has now surrendered a total of 13 seconds over the last three stages which could prove costly in Sunday's concluding stage, a 38-kilometre trial on the streets of Bern.
Pinot will take an overall lead of 34 seconds over Thomas into Sunday’s finale while Slovenia's Simon Spilak is 47 seconds off the lead.