Bolton needed a late equaliser from Abdoulaye Meite to save their blushes against Rabotnicki Kometal in the first leg of their Uefa Cup first-round tie.
Meite scored his first goal of the season for Bolton
The dominant home side wasted several chances as Bolton struggled to cope with the hostile atmosphere in Skopje.
Nicolas Anelka missed an open goal after rounding the keeper just before the break and Nemanja Milisavljevic's strike gave Kometal a deserved lead.
But Meite reacted quickly once Anelka's free-kick was fumbled by the keeper.
Down on confidence after five league defeats in six, Bolton almost made a suicidal error within seconds of kick-off when Jussi Jaaskelainen's mishit clearance of a backpass gave Ivan Trickovski a chance but the striker was unable to react quickly enough.
Sammy Lee was fighting a running battle with the Uefa official on the sidelines, constantly sprinting out of the dug-out to issue instructions, but they did not seem to be having much effect on his toiling players.
Bolton got another slice of luck on 23 minutes when the referee waved away the home side's appeal for a penalty after Meite appeared to handle a cross inside the box.
The performance did little to relieve the pressure on Sammy Lee
Soon after, Nderim Nedzipi's well-hit shot forced a hurried save from Jaaskelainen and Bolton were fortunate that neither of the two Rabotnicki players closing in could get a foot to the loose ball to turn in the rebound.
Rabotnicki's physical approach in midfield and the hostile atmosphere created by a fervent home crowd seemed to rattle Bolton, with Gavin McCann, Gary Speed and Nicky Hunt all collecting bookings within three minutes of each other.
Bolton did finally create a decent chance on 35 minutes, although it was more by luck than judgement with Kevin Davies's mishit shot ending at the feet of El-Hadji Diouf only for the Senegal striker to fire high over the bar.
The best chance of the half went Anelka's way after he latched on to Speed's clever pass and rounded the keeper only to put his shot into the side-netting with the goal wide open.
Denied a morale-boosting goal just before the break, Bolton started the second half sluggishly and needed another sharp Jaaskelainen save to deny Trickovski.
But it was only a temporary reprieve as Milisavljevic fired a superb finish past Jaaskelainen after Bolton's central defenders made a meal of dealing with a routine cross into the box.
Diouf's ball into Speed's path soon after deserved better than the Welshman's clumsy header over the crossbar, but it was a rare attack by a team under the cosh from their fired-up opponents.
Trickovski went close again for a Rabotnicki side who were pressing for a second rather than sitting on their lead.
The Macedonian side's adventurous approach benefited Bolton, and they slowly got themselves back into the match with the hard-working Kevin Nolan and Anelka both going close in quick succession.
And with time running out, Bolton were grateful for a howler from Filip Madzovski after Anelka's free-kick - which should have been saved comfortably - escaped from his grasp, allowing Meite to score from close range.
Bolton boss Sammy Lee:
"What was displeasing was the way we defended.
"We struggled to contend with 50-yard balls launched over the top and that is a concern for me.
"But I was pleased with the effort and the number of chances we created. There were lots of positives and Rabotnicki are a good team."
Rabotnicki Kometal: Madzovski, Stanisic, Vajs, Bozinovski, Lukmon, Demiri, Nedzipi, Osmani (Pejcic 66), Gligorov, Trickovski (Selim 89), Milisavljevic (Velkovski 72).
Subs Not Used: Pacovski, Gjoreski, Mensur, Sabani.
Booked: Milisavljevic, Nedzipi, Osmani, Vajs.
Goals: Milisavljevic 53.
Bolton: Jaaskelainen, Hunt (Joey O'Brien 76), Meite, Cid (Braaten 63), Gardner, Nolan, McCann (Andrew O'Brien 63), Speed, Davies, Anelka, Diouf.
Subs Not Used: Al Habsi, Alonso, Teymourian, Guthrie.
Booked: McCann, Speed, Hunt, Diouf.
Goals: Meite 84.
Ref: Zsolt Szabo (Hungary).