The visitors opened the scoring in the first-half before McFarlane burst into the box and was brought down. He took the spot kick himself and made no mistake, to restore parity after the break.
Bolton scored again, however, with 15 minutes to go and try as they might, Blues couldn't find a way through once more.
The loss - only Blues third in the PDL North - saw Bolton leapfrog Blues into second spot, two points ahead.
Josh Andrews made his return after injury for Blues as a second-half substitute.
Richard Beale, Blues Senior Professional Development Coach, said: "In the first-half we weren't as good as we have been lately.
"In the second, we got on top of them but weren't ruthless enough.
"It was one of those games where the players were probably six out of tens, rather than seven and eights."
Dan Scarr performed strongly in the heart of Blues defence, mentioned Beale, who sent Andrews into the fray in the 65th minute.
Blues: Luyambula, Martin, Burke, Scarr, Bajrami, McCoy, McGilp, Agustien (Boyd-Munce 60 (Forrest 80)), Hurst (Andrews 65), McFarlane, Anderson. Subs not used: Redmond, Amartey.