Trotters boss Sammy Lee somewhat surprisingly opted to leave both Nicolas Anelka and El Hadji Diouf on the bench, with skipper Kevin Davies handed a lone striking role.
Macedonians Rabotnicki started confidently, having earned a 1-1 draw in the first leg at home, before Davies threatened with a far-post effort.
Jussi Jaaskelainen was forced to tip away a Nderim Nedzipi drive after ten minutes as the visitors pushed forward again, before Davies had a shot deflected away for a corner.
Ten minutes before half-time Danny Guthrie's accurate free-kick from long-range forced a smart save from Tome Pacovski, but Bolton were still struggling to find their rhythm.
Davies had a header cleared from close to the line, before the half-time whistle blew with the game still goalless.
Soon after the restart Davies headed wide from a corner as he caused trouble in the air for the visitors, before Stelios Giannakopoulos looked certain to score before a defender got back to block his close-range effort.
Just past the hour mark Lubomir Michalik tried an audacious drive from 45 yards, before Anelka was introduced to a chorus of approval from the home fans.
The Frenchman took just two minutes to make his mark, as he rose at the far post to guide his header from Giannakopoulos' deep cross back across goal and beyond the stranded Pacovski.
Anelka almost latched onto a poor throw-in to double the lead and tested Pacovski late on with a fierce low drive from the right channel.
Diouf nearly played in Giannakopoulos right at the death, but Bolton had done enough to continue their European journey.