The Switzerland international gifted the visitors the only goal of the game with just three minutes played when his poor clearance was converted by Victor Wanyama from long range.
Despite the costly error, Bruce believes that Jakupovic has coped well between the sticks in recent weeks in the absence of injured duo Allan McGregor and Steve Harper.
"It's a shame for the boy today because it's his Premier League home debut and unfortunately he's made a mistake where some goalkeepers get away with it – we see it week-in, week-out with people getting away with it," he told Sky Sports News.
"If Wanyama takes a touch, I think he gets back in his goal and he saves it. Sometimes they end up in row Z, but Eldin's been punished today unfortunately, which is a bit harsh on him."
Hull continue their Premier League campaign next Saturday with a trip to struggling Burnley.