It was Thompson's second goal of pre season after scoring at Merthyr last week.
Vitoria de Setubal opened the scoring in the 14th minute in a match played in the morning sunshine near Nazare, about an hour from the teams base near Lisbon.
Peter Whittingham was not risked as he is nursing a slight calf strain but 17 of the 19 remaining squad members saw some action. Only Darcy Blake and Darren Dennehy were not used.
City finished the game stronger after adjusting to the heat. Vitoria were sharper early on.
"After the first 20 minutes we got into it and it was exactly what we needed," said Dave Jones.
"We played Setubal last season and they have a lot of quality players. They finished fourth in the Portuguese League last season and won the cup.
"Mark Kennedy did well in his first match for us, while Thommo's strike was a superb finish. He almost had two and was only denied a late winner by an outstanding save."
Vitoria de Setubal: B Vale, Janicio, Auri, Hugo, Cissohko, Sandro, Elias, R Chaves, L Lima, B Moraes, Laionel, D Faquira. Subs used: Milojevic (gk), Jorginho, Robson, Michel, B Ribeiro, P Roberto, Mateus, B Gama, Saleiro.
Cardiff City: T Heaton (P Enckelman 62), K McNaughton, T Capaldi (M Comminges 54), R Johnson (D Purse 66), G Loovens, M Kennedy (S Thompson 46), S McPhail, G Rae (R Scimeca 54), J Ledley, P Parry (J Brown 71), R McCormack. Subs not used: D Blake, D Dennehy.