Trotters boss Sammy Lee made three changes from the side which went down 1-0 at Birmingham City in their last league outing, with Kevin Davies, Gerald Cid and Ricardo Gardner coming in for Mikel Alonso, Andy O'Brien and Jlloyd Samuel.
The home side made the early running, with Bolton keeper Jussi Jaaskelainen making a solid block from Nderim Nedzipi's shot just before the half-hour mark, before the rebound went wide.
Wanderers began to find their form after escaping that chance, with Davies threatening with a header from a corner and El-Hadji Diouf firing over when well placed.
Shortly before half-time Nicolas Anelka was released by a fine pass from Gary Speed, but he put his shot into the sidenetting after going past keeper Filip Madzovski.
Soon after the restart Bolton were behind, as their defence failed to deal with a ball into the box and Nemanja Milisavljevic smashed his shot past the stranded Jaaskelainen.
Ivan Trickovski shot narrowly over as the home side attempted to ram home their advantage, having spurned an earlier chance in the opening minute of the second period.
However, Bolton snatched an equaliser with just six minutes to play in Skopje, as Madzovski failed to deal with an Anelka free-kick and Abdoulaye Meite was in the right place to fire home the rebound.
That left Lee's side in pole position ahead of the return leg, with a place in the group stages at stake.