The AG2R rider beat Josef Cerny (CCC) and Michael Rodriguez (Colombia) in a three-man sprint at the end of the morning 128km road stage.
They were part of an early eight-man break and then Rodriguez broke clear from his fellow escapees on the category two climb of Iselsberg, the summit of which was 13.5km from finish.
Bouet crossed the climb 17 seconds behind but bridged the gap on the descent to the finish before producing a turn of speed to record his first victory since the 2010 Tour de L'Ain.
Bouet said: "It is really incredible! Today, I didn’t expect to be in the breakaway and I thought, we'll see what the result is. The breakaway quickly had an advantage of up to six minutes. The gap has increased to nine minutes and with only a 120km long stage, obviously you think to the stage win.
I'm happy because I adopted a very good tactic. I let the Colombian rider get tired in the final climb and the Czech rider run to increase the gap. I know I'm a good sprinter and I was confident in case of a sprint finish.
"I spent three weeks without racing and I return to competition on this Giro del Trentino. My victory proves that you can trust me, that I’m serious when I train and my efforts pay off . During this break, I left home to train to avoid being tempted. It had been two years since I had not won, and some persons doubted to my ability to win but the tide turned!”
Nicola Dal Santo (Ceramiche Flaminia), Josue Moyano (Caja Rural), Pavel Kochetkov (Rusvelo), Jacques Janse Van Rensburg (MTN-Qhubeka) and Gang Xu (Champion System) were also involved in the break that established almost immediately after the start at Tiroler Straße in Lienz.
Their lead was out to nearly nine minutes by the halfway point and Enrico Battaglin (Bardiani Valvole) led the peloton over the line, in ninth place, 6:51 behind the French stage winner.
The 37th edition of the race sees Team Sky's Bradley Wiggins face Vincenzo Nibali (Astana), Cadel Evans (BMC), Domenico Pozzovivo (Ag2r La Mondiale), Ivan Basso (Cannondale), Michele Scarponi (Lampre-Merida) and Stefano Garzelli (Farnese Vini-Selle Italia) as most of the favourites for next month's Giro d'Italia test their legs.
And despite summit finishes on Wednesday and Friday, they have given the breakaway group a big lead in the chase for GC honours in this four-day, five-stage 2.HC race that has attracted a stellar field.
A 14km team time trial follows this afternoon.