The striker, who last month became England’s all-time leading goal-scorer, has missed three days of training after injuring himself during Manchester United’s 3-0 defeat at Arsenal in the Premier League last Sunday.
In his absence, Chelsea centre-back Gary Cahill will captain Hodgson’s side against Estonia at Wembley on Friday, with England having already qualified for next year’s tournament in France after winning all of their eight Group E games to date.
“It’s a disappointment for Wayne, of course,” manager Hodgson told a press conference at England’s team hotel in Watford, north of London.
“He’s not the type of player who likes to miss a game, but unfortunately he received a knock against Arsenal late in the game.
“We’ve been waiting for the ankle to settle down. It’s settling down very well, but we don’t want to risk him tomorrow (Friday).
“He’s got lots of important Manchester United games ahead and I would be devastated if we pushed him out there and something happened to increase the problem with the ankle, so we’ve decided it’s better if he doesn’t play in this game.”
Hodgson described the injury as “minor”.
Rooney, 29, will remain with the England squad this week, but Hodgson said that he will not travel to Lithuania for their final qualifier on Monday.
Tottenham Hotspur striker Harry Kane, Leicester City’s Jamie Vardy and Arsenal’s Theo Walcott are competing to take Rooney’s place up front against Estonia, but Liverpool’s Danny Ings is a doubt with an ankle complaint.
Hodgson said that Ings and Swansea City midfielder Jonjo Shelvey were more likely to feature against Lithuania, but indicated that Michael Carrick will start against Estonia after sitting out Thursday’s training session as a precaution.
The Football Association had earlier confirmed that Rooney will attend the game against Estonia in order to collect a commemorative golden boot for breaking Bobby Charlton’s scoring record.
Rooney eclipsed Charlton’s 49-goal mark with a penalty in a 2-0 win at home to Switzerland and will be presented with the memento by the 1966 World Cup-winner before kick-off. – Agence France-Presse