The striker, who netted the Clarets' equaliser against Chelsea at Stamford Bridge at the weekend, replaced Jakub Pesek in their 7-0 win.
The Sparta Prague winger netted twice for the hosts at the Andrův Stadion in Olomouc — just seconds apart either side of the interval — after Antonin Barak's 26th minute opener.
West Ham United's Tomas Soucek and Filip Novak extended the lead to five before the hour before Jan Sýkora's late double completed the scoring.
Elsewhere, centre back Nathan Collins wasn't given the opportunity to pit his wits against Cristiano Ronaldo at the Aviva Stadium.
The defender was an unused substitute as the Republic of Ireland held Group A leaders Portugal to a goalless draw in their penultimate World Cup qualifier in Dublin.
Former Burnley midfielder Jeff Hendrick also featured, making way for Conor Hourihane just three minutes before the visitors were reduced to 10 men following Pepe's dismissal.