The experienced front man fired confidently home in the dying seconds of the game after debutant Hidetoshi Nakata had got the slightest of flick on's following a left-wing cross by impressive substitute Fabrice Fernandes.
Plovdiv had a large chunck of the possession in the first half and where to play with a lot of confidence in front of quite a generous away following who had made the long trip from Bulgaria.
Tunisian defender Radhi Jaidi had the first chance of the game on four minutes but the Bolton man could not get enough direction on his header following a free kick from Nakata.
Jaidi's defensive partner Bruno N'Gotty then mis-timed his downward header from Stelios Giannakopoulos right wing corner but the veteran Frenchman saw luck on his side as the effort went out for a corner
Plovdiv took the lead against the run of play shortly before the half hour mark as a right wing cross by veteran utility player Vladimir Ivanov was fired home by Macedonian attacker Boban Janchevski
The actions of some of the Loko players caused the Bolton people to become restless as the medical stretcher was unnecessarily brought onto the field of play for around a dozen times throughout the evening.
Bolton tried to get the ball up to main striker El-Hadji Diouf but his path was often blocked by some attentive defending by the Loko backline of Robert Petrov and Vladimir Djordani
After half time the hosts came out of the blocks with some renewed optimism and this nearly paid off just five minutes into the second half as Ivan Campo saw his low shot well saved by Stoyan Kolev in the Loko goalmouth
Kolev often came to punch the ball and seemed less assured when Bolton where on the attack but the previously mentioned Petrov and Djordani kept any panic to a minimum.
That was until Bolton manager Sam Allardyce decided to up the stakes by bringing on eventual hero Borgetti for Henrik Pedersen and both Kevin Nolan and Fabrice Fernandes for captain Jay-Jay Okocha and Stelios Giannakopoulos, both of whom seemed less involved on their return to the European stage.
Nolan and Fernandes breathed new life into the Wanderers, with Fernandes in particular proving to be cheif tormenter down the Plovdiv left hand side on his Bolton debut.
On 72 minutes Bolton's second half persistance finally paid off as fans favourite El-Hadji Diouf stooped at the far post to head home a deep right wing cross by England U21 full back Nicky Hunt.
This goal was to change Bolton's overall approach to the game and certainly lifted the home supporters who had made the stadium a fortress in the final quarter of the game.
Plovdiv protested strongly as they felt that one of their players had been fouled by Bolton substitute Kevin Nolan in the build up to the goal but referee Darko Cererin waved away any appeals.
New boy Fernandes then had the first of two chances to put his new club in front, the first of which was all his own work after he teased and tormented the Plovdiv defenders before firing over the crossbar.
The second Fernandes chance came in the final minute of the game, this time an inch nearer as goalkeeper Kolev outstretched to tip the ball over for a corner. The former Fulham, Rangers and Southampton player was certainly enjoying his return to first team action following nearly nine months in the wilderness at his previous club.
Borgetti was the hero of the hour though as he struck right at the death to give the Wanderers a famous and historical victory in their first ever UEFA Cup game which will conclude with a difficult trip to Bourgas in two weeks from now
Bolton Wanderers: Jussi Jaaskelainen, Nicky Hunt, Radhi Jaidi, Bruno N'Gotty, Henrik Pedersen (Jared Borgetti), Hidetoshi Nakata, Ivan Campo, Jay-Jay Okocha (Kevin Nolan), Stelios Giannakopoulos (Fabrice Fernandes), El-Hadji Diouf, Ricardo Gardner
Subs not used: Ian Walker, Kevin Davies, Joey O'Brien, Abdoulaye Diagne-Faye
Lokomotiv Plovdiv: Stoyan Kolev, Kiril Kotev, Robert Petrov, Vladimir Djordani, Aleksandur Tunchev, Vladimir Ivanov, Georgi Iliev (Yavor Vundev), Krasimir Dimitrov, Ivan Krizmanic, Iljami Halimi (Daniel Georgiev), Boban Janchevski (Metodi Stoynev)
Subs not used: Vasil Kamburov, Velko Hristev, Hristo Zalatinski, Ivo Mihailov
REFEREE:
Darko Ceferin
ATTENDANCE:
19,723
BOOKED:
Hidetoshi Nakata (Bolton)
Boban Janchevski (Plovdiv)
Georgi Iliev (Plovdiv)
Vladimir Djordani (Plovdiv)
Ricardo Gardner (Bolton)
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