Playing their second game at the Stadion Lind in the Austrian town of Villach, Mauricio Pochettino's men had found themselves trailing to Muhammed Demirci's 62nd-minute stunner.
But quick-fire half-volleys from substitutes Rickie Lambert and Emmanuel Mayuka turned the game on its head, with youngster Lloyd Isgrove putting the cherry on the cake in the final minute with his maiden senior-level goal for the Club.
Lambert's 75th-minute strike was his first this pre-season, while Mayuka's stunner three minutes later ended his wait to open his Saints account since moving to St Mary's last August.
As he has for his squad's first three friendlies, manager Mauricio Pochettino shuffled his pack once more, with Artur Boruc returning between the sticks after being left out of last Wednesday's defeat to FC Schalke 04.
With Nathaniel Clyne out with an injury picked up on the training ground, Calum Chambers started at right-back for the fourth game in a row. José Fonte, Jos Hooiveld and Danny Fox made up the rest of the defence.
Saints' midfield trio consisted of Jack Cork, Morgan Schneiderlin and James Ward-Prowse, while Guly returned from a groin injury to join Adam Lallana in supporting frontman Jay Rodriguez.
The game began to a soundtrack of incessant noise from the travelling Beşiktaş fans, although the 50-or-so Saints supporters present certainly did their best to make themselves heard.
It took until the tenth minute for either side to fashion a chance, and it was the Turkish outfit who went close as Manuel Fernandes's free kick found the head of Hugo Almeida, but Boruc pulled off a magnificent save to turn the ball around his left-hand post.
There was plenty of good build-up play from Saints, but it took until the 38th minute for them to summon their first shot on target as Guly led a rapid break and played the ball to Fox via Cork, but the left-back's low effort was held by Cenk Gönen.
The Beşiktaş stopper had to be at his best barely 60 seconds later when, after Rodriguez had been felled right on the edge of the area, he tipped Ward-Prowse's well-hit free kick just wide of the post as the half drew to a lively close.
HALF TIME: SOUTHAMPTON 0-0 BEŞIKTAŞ
Pochettino made three changes at the break, bringing on Luke Shaw, Victor Wanyama and Lambert for Fox, Chambers and Guly.
But it was a Beşiktaş substitute who had the first chance of the new half as Dentinho found himself perfectly-poised to tap in Gökhan Töre's cut-back only to side-foot the ball over Boruc's crossbar.
Former Portsmouth midfielder Fernandes then went close, before lone front-man Almeida tested Boruc with a fierce near-post effort.
Saints brought on Steven Davis and Jason Puncheon just before the hour, but it was Beşiktaş who would open the scoring on 62 minutes as DEMIRCI – a half-time replacement of their own – took over possession in midfield before unleashing an unstoppable 30-yarder into the top left-hand corner.
With 20 minutes to go, Mayuka and Isgrove were summoned from the bench along with Dejan Lovren, and the former immediately looked dangerous.
The Zambian, who had not scored at any level for the Club since joining at the end of the summer transfer window last year, had the ball in the net on 73 minutes but his close-range finish was adjudged to have come from an offside position.
Instead it was LAMBERT who levelled matters with a quarter-of-an-hour to play, taking Cork's right-wing free kick on his chest before slamming beyond Gönen for one-all.
Better was to follow three minutes later, though, as Lambert dinked the ball into the path of MAYUKA, who did not hesitate in lashing a left-footed half-volley in from a tight angle to give Saints the lead.
Southampton should have found their third with four minutes remaining as Davis seized possession on half-way and ran clear on goal but could only look on as his delicate chip bounced off the crossbar and was claimed by Gönen as Mayuka lurked.
The winning margin would be extended with the final kick of the game, though, as Shaw surged down the left and centre for the onrushing ISGROVE to slide home to round off a good performance and a positive trip away for Saints' First Team.
FULL TIME: SOUTHAMPTON 3-1 BEŞIKTAŞ
Saints team: Artur Boruc, Calum Chambers (Victor Wanyama 46), José Fonte, Jos Hooiveld (Dejan Lovren 70), Danny Fox (Luke Shaw 46), Jack Cork, Morgan Schneiderlin (Steven Davis 58), James Ward-Prowse (Lloyd Isgrove 70), Guly (Rickie Lambert 46), Adam Lallana (Jason Puncheon 58), Jay Rodriguez (Emmanuel Mayuka 70). Unused substitutes: Paulo Gazzaniga (GK), Jordan Turnbull, Jack Stephens.
Goals: Lambert (75), Mayuka (78), Isgrove (90)
Beşiktaş team: Cenk Gönen, Serdar Kurtulus, Tomas Sivok, Pedro Franco, Ersan Gülüm (Gökham Süzen 46), Veli Kavlak, Oğuzhan Özyakup (Muhammed Demirci 46), Manuel Fernandes, Gökhan Töre (Ibrahim Toraman 73), Olcay Şahan (Dentinho 46), Hugo Almeida (Mustafa Pektemek 63). Substitutes: Günay Güvenç (GK), Mehmet Akgün, Julien Escudé, Necip Uysal, Tanju Kayhan.
Goal: Demirci (62)
Booking: Süzen (75)