England retain their unbeaten record in Group F.
Versatile Zimbabwe-born forward has broken his arm for the third time in less than a year.
Bangladesh host England in the third ODI on 12 October. The three match series is tied at 1-1.
England lead Slovenia by two points in the group.
Rooney, 30, admits he is going through one of the most difficult periods of his career.
England caretaker manager Gareth Southgate has confirmed the captain will be named on the substitutes' bench.
Three Lions skipper is expected to be demoted for Tuesday's World Cup qualifier in Ljubljana.
Eddie Jones is set to meet with Premiership directors after criticism of costly recent training camp.
Meanwhile, Mashrafe Mortaza and Sabbir Rahman have both been fined 20% of their match fees.
The Sunderland goalkeeper will travel to Ljubljana as understudy to Joe Hart and Fraser Forster.
The three match series is tied at 1-1 with the third ODI scheduled for 12 October at Chittagong.
Rooney, 30, was booed by a section of the Wembley crowd during England's 2-0 win over Malta.
The Tigers win by 34 runs as Mashrafe Mortaza takes four wickets in Dhaka.
England face Slovenia in the next World Cup qualifiers on 11 October.
The caretaker boss refuses to drawn on Jose Mourinho's belief Rooney is unsuitable for holding role.
Hosts produce underwhelming display at Wembley to make it two wins from two in World Cup qualifying.
Bangladesh host England in the second ODI on 9 October. The visitors lead the series 1-0.
Arsene Wenger is on the final year of his contract with Arsenal.
Adil Rashid finishes with figures of four for 49 as hosts throw away chances of victory with late collapse.
Gareth Southgate has declined to call up a replacement, despite Gary Cahill suffering from a sore throat.
West Indies will be the visitors to Birmingham in historic match in August 2017.
Spaniard backs the Gunners to win the Premier League this season.