The look in José Pekerman’s baffled pinched eyes said it all. Colombia had just made history by qualifying for consecutive World Cup knockout stages for their first time, but the worry creased across the coach’s furrowed brow when asked about the extent of James Rodríguez’s latest injury was plain to see.

“I’m very concerned, it’s very worrying,” the 68-year-old Argentinian confessed after Colombia’s 1-0 win over Senegal in which Rodríguez had to depart the field with a frustrated thumping of the turf just 31 minutes in. “It’s a very difficult situation for us. I don’t know where he stands right now. I can’t say any more because I just don’t know.”

Arms folded and fingers twitching on the desk in front of him, Pekerman’s subtle mannerisms are usually telling. For Colombian journalists, every flicker of emotion shown by the highly hermetic coach is carefully interpreted. And this wasn’t good. “You could see it in Pekerman’s face, he fears the worst,” observed one reporter on the shuttle bus back to town. “I think we’re probably going to have to do this without him [Rodríguez].”

The calf strain that had already sidelined the on-loan Bayern Munich midfielder from starting Colombia’s opening match against Japan again seems to be the issue. He did not train on Saturday but the Colombian Football Federation later said in a statement that a scan had shown swelling but no muscle tear. After Rodríguez missed training in the run-up to the tournament, at Colombia’s isolated base on the banks of the River Volga some 25 miles from Kazan, one coach commented that the player was feeling pain every time he started jogging. Not wanting to risk doing lasting damage and potentially missing the whole tournament, he had requested to take it easy.

This was not the first time he had suffered a problem with the same troublesome left calf. Against Besiktas in Bayern Munich’s Champions League game in February he was clutching the calf when substituted just before half-time. He ended up missing three weeks.

Pekerman claims that Rodríguez had trained normally before the Senegal match and was thus left confused by what the real issue was. Even in a best-case scenario Rodríguez will not be 100% fit for Colombia’s date with England in the last 16 in Moscow on Tuesday. For Colombia and their Argentinian coach, that is desperately concerning.

Colombia have come so far since the guileful coach dropped the No 10 jersey in the lap of Rodríguez upon taking over as Los Cafeteros coach in January 2012. Back then, Rodríguez had only three caps for his country and was just 21 years old. This was an extraordinary statement and a resounding show of support in somebody so young.

José Pekerman has put increasing trust in Juan Quintero for Colombia. Photograph: Max Rossi/Reuters

Pekerman had inherited a team that had spent 16 years trundling in world football’s wilderness. In the perennial search for an heir to Carlos “El Pibe” Valderrama, three World Cup qualifying campaigns had slid from view. For all its romance and mystique, many a precocious star had buckled under the weight and responsibility of the No 10.

Yet with Rodríguez, Pekerman knew what he was doing. In his first managerial role in the 1990s, he led Argentina Under-20s to three world youth titles. When later promoted to the senior team, Pekerman would give an 18-year-old Lionel Messi his international debut. Rodríguez was clearly in good hands.

Six years on and the coach’s faith in his prodigy has been more than justified. Already joint-third top scorer for his country and still only 26, Rodríguez’s achievements in yellow are remarkable. Of Colombia’s last 15 goals at the World Cup, the playmaker has scored six and provided four assists. In his astonishing World Cup debut four years ago he scored the best goal, won the Golden Boot and was arguably the tournament’s best player as Colombia reached the last eight for the first time. No player has been so important in Colombia’s football history. Not Valderrama, nor Faustino Asprilla, nor even Radamel Falcao.

Pekerman signed a new four-year contract with Los Cafeteros in July 2014 and immediately began building a new side around his star. But qualification for Russia 2018 was a slog. Opponents routinely frustrated Colombia by sitting deep and stifling their attacking play.

As a wandering No 10, Rodríguez floated between the lines seeking to influence a game starved of space. Gone was the swashbuckling and fast-transition football tied to neat geometrical patterns that Colombia served up in Brazil. Now Pekerman’s side were often dependent on some Rodríguez magic to swing games. Indeed, of 21 goals Colombia clocked up in qualifying, Rodríguez was involved in 48% of them (again six goals and four assists).

That creative reliance may now pose a problem as Colombia plot victory against England without their mercurial star. Curiously, Pekerman’s long-term backup to Rodríguez had been Edwin Cardona, a bulky but technically gifted midfielder who was chopped from Colombia’s 23-man squad without formal explanation.

Unofficially though, Cardona’s fate was sealed when he received a five-match ban from Fifa after making a racist gesture against a South Korea player in a November friendly, before then being implicated in a scandal at Boca Juniors that involved “girls, alcohol and knives”.

Pekerman was unimpressed and instead turned to the tortured genius of Juan Quintero, who will now assume responsibility for picking apart England’s defence.

Four years ago, Colombia’s World Cup plans were also dealt a crushing blow when their talisman striker Falcao suffered an anterior cruciate ligament injury. Pekerman found a way of juggling his side to thrive without a player who had finished as his country’s top scorer in qualifying. But Colombia without Rodríguez is a very different prospect. And it may prove to be Pekerman’s biggest challenge yet.