Recent arrival Vakoun Bayo had the first sight of goal after Tom Dele-Bashiru pressed high to retrieve possession. The Ivorian’s effort was low and powerful, but hit the side-netting.
Lee put the visitors ahead five minutes later with a first-time finish inside the box.
Hassane Kamara linked up effectively with João Pedro following the opener. The latter fired across goal for Dan Gosling to tap home, only for the assistant referee to raise his flag for offside.
Bolton’s lead doubled just before half-time through Afolayan on the right flank, with the 24-year-old driving inside and tucking his shot past Daniel Bachmann.