England dominated in Saint-Étienne, but couldn't find a way past resilient Slovakia.
Despite a host of chances, the Three Lions were held to a 0-0 draw, which sees them qualify for the Last 16 in second-place.
England manager Roy Hodgson made six changes for the match, with captain Wayne Rooney among those dropping out.
Napoli captain Marek Hamšík was once again deployed in a deep midfield role in a 4-3-3 shape for Slovakia.
The first chance fell to the Three Lions, but Peter Pekarik’s fantastic last-ditch block prevented Daniel Sturridge from opening the scoring.
Jamie Vardy was in for Harry Kane, and he raced onto a long ball, but Matúš Kozáčik was off his line quickly to block his shot.
Ryan Bertrand was lucky to avoid a red card for an elbow on Pekarik which left the Slovakian defender bleeding.
Adam Lallana had the chance to open the scoring just after the half-hour mark, but he hit it straight at the Slovakian goalkeeper after Clyne found him on the edge of the box.
England had dominated the first half but they should have been behind when Chris Smalling chested the ball down for Robert Mak.
The Manchester United defender was relieved as Mak failed to connect and Joe Hart managed to clear.
Dele Alli replaced Lallana, and almost scored immediately, but Martin Skrtel cleared his effort off the line.
England kept up the pressure, with Sturridge failing to connect properly with Eric Dier’s lofted through-ball.
Slovakia decided to settle for the draw, taking off Vladimír Weiss for Sampdoria defender Milan Škriniar.
It wasn’t pretty, but it was effective as Ján Kozák’s side held on for a goalless draw which secures third-place.
England are through to the Last 16, but Slovakia must wait to see whether they will be ranked as one of the four best third-place sides.
Slovakia 0-0 England
Slovakia: Kozáčik; Pekarik, Škrtel, Ďurica, Hubočan; Kucka, Pečovský (Gyömbér, 66), Hamšík; Mak, Duda (Švento, 57), Weiss (Škriniar, 78)
England: Hart; Clyne, Cahill, Smalling, Bertrand; Henderson, Dier, Wilshere (Rooney, 56); Lallana (Alli, 60), Vardy, Sturridge (Kane, 76)
Referee: Carballo [ESP]