Lee made seven changes for a match he simply could not afford to lose in the wake of the Trotters’ woeful start to their Barclays Premier League campaign.
With Sunday’s crunch visit of Chelsea in mind, key players such as Gary Speed and Kevin Nolan, Ricardo Gardner were rested while influential strike duo Anelka and El-Hadji Diouf started on the bench.
It was a bold gamble one which at times threatened to backfire spectacularly against the Macedonian league leaders.
But Anelka’s sixth goal of the season, a looping header from a cross from fellow substitute Stelios Giannakopoulos, settled the Trotters’ nerves.
Anelka, 28, committed to the club in August by signing a new deal keeping him at the club until 2011. Anelka’s latest vital strike, which came just two minutes after his arrival, allowed Lee to breath a little easier.
That the Trotters boss has found life tough since replacing Sam Allardyce in April is undeniable, with just one Barclays Premier League victory from 10 attempts proof enough.
Danny Guthrie, on a season-long loan from Liverpool, produced a delightful flick in the centre circle after six minutes which allowed Mikel Alonso stride forward at pace with the ball.
Alonso embarked on a strong run down the right flank and whipped a teasing cross to the far post for Kevin Davies but his outstretched boot failed to make any meaningful contact.
Yet Bolton’s momentum were building and midway through the opening period Daniel Braaten raced clear down the left and delivered a deep cross which Guthrie narrowly failed to connect with at the far post.
In the 32nd minute Davies greeted Guthrie’s right-wing corner with a firm header which a visiting defender hacked off the line.
Lazar Stanisic hauled down Braaten on 35 minutes 25 yards from goal and Guthrie whipped in a fierce free-kick which drew a smart from Pacovski at his near post.
Lee replaced Alonso at the break with Stelios and the Greek winger wasted little time making his presence felt. In the 55th minute he latched on to a Davies flick before rounding Pacovski and hitting the post.
In the 66th minute Anelka replaced Davies and within two minutes scored.
Stelios did superbly well to fashion the space to send over a deep cross from the left flank and Anelka rose above Stanisic to nod home into the far corner.
Anelka proved a constant menace thereafter and refused to allow Rabotnicki’s defence to settle. He chased lost causes and caused untold panic and the only question Bolton fans wanted answered was why he was not on from the start
Jaaskelainen, Joey O’Brien, Andrew O’Brien, Michalik, Cid, McCann, Braaten (Diouf 75), Guthrie, Alonso (Stelios 46), Wilhelmsson, Davies (Anelka 66).
Pacovski, Kovacevic, Stanisic, Vajs, Lukmon (Bozinovski 75), Milisavljevic, Demiri, Osmani (Velovski 46), Gligorov, Nedzipi, Trickovski (Pejcic 63).
T Skjerven (Norway).