But Bolton took the lead soon after the break when Gretar Steinsson collected a Kevin Davies pass and shot through Mark Bunn's legs from a narrow angle.
Charlton's best chance in a fairly tame first half came on the half-hour mark when Nicky Forster's flick-on was met by Deon Burton's ferocious volley from a tight angle but Shane Higgs made a reflex save to turn it past the post.