The five-time world champions were aiming to put Saturday's disappointing 1-1 draw with Panama in Porto behind them but it was the Czechs who initially showed the attacking flair and took the lead through David Pavelka.
Robert Firmino equalised for the visitors just after the break and forward Jesus came on for Philippe Coutinho in the 72nd minute to secure the victory with two goals in seven minutes.
"The first half was harder and the performance was not consistent. We made changes into the second half and the players were able to pass more," said Brazil coach Tite.
"I saw more determination from (Jesus) to take part in the game, to get to the goal and more willingness to create and also to finish."
The hosts, who made four changes from the side that were thrashed 5-0 by England in their Euro 2020 qualifier on Friday, took the lead in the 37th minute when a deflected pass fell to Pavelka, who shot first-time past keeper Alisson.
Brazil -- playing without injured forward Neymar -– levelled when Czech halftime substitute Theodor Gebre Selassie misplaced a pass straight to Firmino, who held off a defender and slid the ball into the net.
The visitors continued to turn up the pace and grabbed the lead in the 83rd minute when Brazil substitute David Neres crossed to Jesus, who went on to wrap up the win in the final minute.
Czech manager Jaroslav Silhavy said his team had paid the price for not keeping up the pressure in the second half, which allowed Brazil to take charge.
"We couldn’t keep the fast pace from the first half when we played very intensely and the Brazilians often did not know what to do with us," Silhavy said. "The equalising goal put the opposing side in the saddle. It was our mistake."
Brazil's match against the Czechs was their last scheduled friendly before they open their Copa America campaign against Bolivia in the group stage in June.
(Reporting by Robert Mueller, Writing by Michael Kahn, Editing by Ken Ferris/Nick Mulvenney)
