Luis de la Fuente made seven changes from the side that beat Croatia, yet his much-changed team still controlled the game from start to finish, ending the night with 70% possession, 704 passes and 22 shots. Baena broke the deadlock in the 39th minute, firing home from the spot after VAR penalised Lukas Ambros for handball, while Pau Cubarsi and Fabian Ruiz both struck the woodwork in the first half.
Yeremy Pino had a second goal ruled out for offside early in the second half, and Czechia were reduced to ten men in the 72nd minute when captain Ladislav Krejci was sent off for denying Roberto Fernandez a goalscoring opportunity, his yellow card upgraded to red after a VAR review. The hosts had their moments from set pieces, with Adam Hlozek heading against the bar, but they failed to register a single shot on target. Fernandez hit the post deep into stoppage time before Pubill pounced moments later to seal a fifth straight group win, leaving top spot in Group A3 to be settled when Spain face England on Sunday.
Here are the Spain player ratings from the epet Arena...
Goalkeeper & Defence
Unai Simon (7/10): The captain was barely tested, with Czechia failing to hit the target all night. He was alert to claim crosses into his box and launched the long ball that sent Pino through for his disallowed goal early in the second half.
Pedro Porro (7/10): Busy down the right, combining well with Pino and creating an early chance for Ferran Torres. His night was soured slightly by an 11th-minute booking after Lukas Provod turned him, and he was replaced by Pubill in the 76th minute.
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Pau Cubarsi (8/10): Calm at the back and composed in possession. Came closest to scoring for Spain in the first half when he headed Marc Cucurella's cross against the bar in the 31st minute.
Dean Huijsen (7/10): Brought the ball out confidently and went close twice with headers from Baena's deliveries, forcing Matej Kovar into a save in the 22nd minute. Tracked back well to stop Ryan Naderi running in behind, but his foul handed Czechia the free-kick from which Hlozek hit the bar.
Marc Cucurella (8/10): Spain's most dangerous full-back. Pounced on a loose pass from Krejci to fire just wide in the first half, delivered the cross for Cubarsi's header against the bar, and set up Fernandez for a close-range chance in stoppage time.
Midfield
Martin Zubimendi (7/10): Playing in a protective mask, he kept Spain ticking at the base of midfield with tidy, efficient distribution, helping the visitors keep Czechia pinned in their own half for long spells.
Fabian Ruiz (7/10): Linked play well alongside Zubimendi and was unlucky not to score when his curling effort from Fermin Lopez's pass came back off the post in the 41st minute. Replaced by Pedri in the 76th minute.
Fermin Lopez (7/10): Lively between the lines, he set up Ruiz's effort against the post and Ferran's blocked shot, and tried his luck from distance without troubling Kovar. Made way for Jorge de Frutos in the 82nd minute.
Attack
Yeremy Pino (7/10): Started on the right with Lamine Yamal sidelined and thought he had doubled the lead in the 48th minute with a neat dink over Kovar, only for VAR to rule it out for offside. Teed up Fermin for a shot before being replaced in the 66th minute.
Alex Baena (8/10): Man of the match. Took responsibility from the spot and coolly converted to open the scoring. His crosses created both of Huijsen's headed chances, he forced Kovar into a save in the second half, and he teed up Fernandez's effort against the post in stoppage time.
Ferran Torres (6/10): Got into good positions but wasted them, firing wide twice in the opening 20 minutes and seeing another effort blocked after a Fermin pass. Replaced by Fernandez in the 66th minute.
Substitutes & Manager
Roberto Fernandez (7/10): His run drew the foul that led to Krejci's red card. Should have scored in stoppage time when he could not sort his feet out from close range after Cucurella's cut-back, then hit the post from Baena's pass moments before Pubill's goal.
Mikel Merino (6/10): Came on for Pino in the 66th minute and was booked for dissent shortly afterwards, protesting Krejci's initial yellow card. Helped Spain keep control in the closing stages.
Pedri (6/10): Replaced Ruiz in the 76th minute and kept the ball moving without making a major mark on the game.
Marc Pubill (8/10): Replaced Porro in the 76th minute. Fired high and wide from De Frutos' pass in stoppage time, then won the ball high up the pitch as Czechia tried to play out from the back and slotted into the bottom corner in the sixth minute of stoppage time.
Jorge de Frutos (6/10): Replaced Fermin in the 82nd minute and set up Pubill's first effort as Spain pressed for a second.
Luis de la Fuente (7/10): Made seven changes and still saw his side dominate. Spain could have been out of sight earlier given how often they hit the woodwork, and they were vulnerable at set pieces, but his decision to bring on Pubill paid off late on.