City were again well represented with Demi Stokes, Jill Scott and Keira Walsh all in the starting line-up, Lauren Hemp featuring as a second half substitute with Gemma Bonner, Georgia Stanway and Ellie Roebuck also on the bench.
The occasion was a stark contrast to last Saturday’s Wembley showpiece against Germany which attracted a record turnout of 77,000.
And on a snowy, cold night in Ceske Budejovice in front of a sparse crowd, Phil Neville’s side made a shaky start and found themselves trailing on 15 minutes.
Poor marking from the Lionesses allowed Katerina Svitkova the opportunity to run at the visitors, and her deft through ball found Tereza Szewieczkova who coolly lifted the ball over Carly Telford.
England though regrouped and a two-goal salvo inside five minutes saw the Lionesses storm into the lead.
First on 15 minutes, Beth England latched onto Nikita Parris’ cut-back and despatched a instinctive right foot volley from an acute angle into the roof the goal.
On 20 minutes, the Lionesses struck again to take the lead. Lucy Staniforth had the vision to find the unmarked Beth Mead and the Arsenal striker showed great composure to steer the a superb shot into the right hand corner of the net.
However, England’s advantage was shortlived as Szewieczkova struck for her second goal of the match to draw the hosts level.
Mead then had the ball in the Czech net again on the hour as England turned up the second half pressure but her deflected header was ruled out for a foul in the build up by Scott.
Three minutes from time however, the Lionesses claimed the win when Leah Williamson drilled home a low shot from just outside the box past Czech keeper Barbora Votikova.
Elsewhere, Tessa Wullaert played 90 minutes and provided an assist as Belgium beat Lithuania 6-0 in a Euro Women's 2021 qualifier.
Meanwhile, Tyler Toland was an unused substitute as the Republic of Ireland drew 1-1 away to Greece in their Euro 2021 qualifier while Matilde Fidalgo was also an unused sub as Portugal drew 1-1 with Finland in their latest Euro tie
City are back in FA Women's Super League action against West Ham on November 17th. Kick-off at the Academy Stadium is 12.30pm and tickets are available.