Mateo Kovacic completed 90 minutes and recorded an assist for Croatia, who won to finish second in the group whilst Reece James was an unused substitute for England as they topped Group D.
Mason Mount, Ben Chilwell and Billy Gilmour were not involved as the trio are self-isolating following Gilmour's positive COVID-19 test.
Who featured and what happened?
Czech Republic 0-1 England | Group D - Matchday 3
No Chelsea players featured as England ran out winners to top Group D.
England were nearly ahead early on as Luke Shaw fed Raheem Sterling and the winger chipped the ball past the Czech goalkeeper but his shot was kept out by the post.
Sterling did find the breakthrough moments later as Jack Grealish's cross was floated towards the far post and the Man City winger headed home.
In a fairly uneventful second half, England had a goal disallowed later on as substitute Jordan Henderson was denied due to an offside call.
Croatia 3-1 Scotland | Group D - Matchday 3
Both teams needed a win for any chance of qualification as Kovacic started for the Croatians. Gilmour was not in the squad after testing positive for COVID-19.
It was Kovacic's team who were ahead just 17 minutes in, former Everton man Nikola Vlasic firing home from inside the box.
The Scots levelled just before half time through Celtic's Callum McGregor, his low driven shot from outside the area finding the back of the net.
The Croatians restored their lead in the second half as Kovacic registered an assist. Real Madrid's Luka Modric receieved the ball from the Chelsea midfielder on the edge of the area and his curling strike from outside the box beat David Marshall. Kovacic's weight of pass was perfect, allowing Modric to adjust his body and find the finish.
Ivan Perisic put the nail in Scotland's coffin, glancing in after a near post run from a corner to add a Croatia third.
The results see England progress to the Round of 16 as group leaders whilst Croatia also progress in second place. Czech Republic will have to wait to see if they are to qualify as one of the best third placed teams.