Gretar Steinsson and Johan Elmander scored the goals for the Reebok men, who had to work hard before eventually getting the better of a side just seven places below them on the league ladder.
The Blades were forced into a late change when Dutchman Marcel Siep pulled up with a hamstring injury in the warm-up, to be replaced by Jonathan Fortune.
And after a fragmented start, Bolton forged the first real chance as Tamir Cohen and Kevin Davies exchanged passes on the right to crate a shooting opportunity for Ivan Klasnic, whose effort was saved at the second attempt by Mark Bunn.
Sheffield United hit straight back and Henri Camara should have opened the scoring when he went clear through on Lee Williamson's clever ball only to lob his shot over Jussi Jaaskelainen and the crossbar.
At the other end, makeshift winger Jlloyd Samuel also got a clear sight of goal but having beaten Chris Morgan once, he opted to check back again, allowing the Blades defender to scramble the ball clear.
The Championship side continued to shade possession and chances throughout the first half and Morgan might well have put his side ahead when he climbed above Gary Cahill to reach Stephen Quinn's cross only to head just wide.
Whatever manager Owen Coyle said at the break, however, seemed to pay instant dividends as within two minutes of the restart, his side were ahead.
Chung-Yong Lee powered through the middle, dropping the ball off with Davies who threaded a perfect pass to Steinsson and while the Icelander looked odds on to cross, he cleverly slipped a shot under Bunn's legs to register his first strike of the season.
Bolton nearly made it two and few minutes later when Cahill seized on a knock down from Klasnic on the edge of the area and drove a shot that nicked off Fortune and bounced just wide of the post.
The Premier League strugglers were defending well too, with Zat Knight making a telling contribution on 64 minutes to get his head to Darius Henderson's excellent cross towards Camara.
Kevin Blackwell threw on Jamie Ward and Richard Cresswell in search of a goal but it was a Bolton substitute that settled the tie, as Elmander came off the bench for the third time this season to score.
There looked a hint of offside as Chung-Yong played the Sweden international in down the right but there was no mistake about his finish which nestled nicely inside the far post.