There were already doubts over the pair and now it has been confirmed they will be missing.
A foot problem kept Reid out of Monday's win over Birmingham and now Howazrd has suffered a knee injury.
The pair join Bobby Hassell and Adam Eckersley on the missing list with Martin Devaney also expected to pull out with an Achilles problem
Simon Davey told www.barnsleyfc.co.uk:
"Brian has a knee injury and Paul has not recovered from his foot problem. They are both out of the game against Southend but we are hopeful for the week after. Martin Devaney is also touch and go for Saturday with an Achilles problem but we will give him right until the last minute to prove his fitness although we are planning on being without him".