After a 2-1 success over Bootle in the League on Saturday, United lost out to the Bucks in the Liverpool Senior Cup Quarter Final with a 3-1 defeat at the Berry Street Garage Stadium.
Both sides were subject to changes due to ineligibility with Paul McNally bringing Cameron Glennon, Ben Stanton, Khalil Osi-Efa, Tom Grimshaw and Emini Adegbenro into the lineup.
Bootle started the brighter with Rob Doran heading a Liam Loughlin cross past the post before a through pass from Alex Griffiths found Emini Adegbenro who advanced on goal and drew a low save from Ryan Jones who tipped Tom Croughan's header over the bar a minute later.
Croughan had two further chances as he sent a shot past the post before a great combination of Jason Carey and Griffiths put the forward in on goal and he forced a strong stop from Jones. The hosts opened the scoring on the half-hour with Loughlin's pass cannoning off several players from both sides before Steven Jones flicked past Ben Barnes for 1-0.
United levelled on 34 minutes as Callum Preston's corner was flicked on at the far post by Khalil-Osi-Efa for Emini Adegbenro who fired past Jones for 1-1. Bootle went close to regaining lead with Doran's header from a corner drawing a superb tipping save from Barnes onto the crossbar.
Skem went into the interval behind as a teasing cross from Carberry was unfortunately hit into the net by a sliding Osi-Efa as he looked to hit past the post making it 2-1.
The second half saw John Connelly head a Carberry cross past the post before he went closer on 62 minutes from the same position, connecting to Doran's looping cross to slot past Barnes for 3-1.
United had chances to reduce the deficit with Carey and Adegbenro going close and a Preston corner forcing a double save from Jones before substitute Lee Hughes forced a strong save from Barnes at the other end.
Skem continued to threaten with a shot on the edge of the area from Griffiths forcing Jones into a fingertip save over the bar. The final whistle minutes later saw Bootle held on for the victory and secured a place in the last four with United reflecting on a mixed performance overall and a strong double header this week against the Bucks.
Bootle- R.Jones, Halligan, Carberry, Hoy, Cartwright, Millington, Doran, Loughlin (c), S.Jones ( Hughes 68), Foy, Connelly (Williams 79). Subs not used - McGovern, Brady, Hamilton.
Skelmersdale United - Barnes, Glennon ( Staunton 87), Preston, Osi-Efa, Stanton, Tyrer (c), Griffiths, Carey, Croughan ( Ellis 73), T.Grimshaw ( J.Grimshaw 62), Adegbenro. Subs not used- Brodie, Davies.
Att-133