The pair, aged 24 and 29, have been questioned by the North East Counter Terrorism Unit on suspicion of offences under the Terrorism Act.
Officers have today been granted warrants to hold them for a further seven days.
A third man, a 23-year-old from Sheffield arrested for assisting an offender, was yesterday released without bail while under investigation.
“There are no connections to the recent incident and investigation in Manchester,” police stressed in a statement after the raids were carried out.
“The operation is based on recently received intelligence.”
Residents living nearby the homes raided on Thursday had reported being startled by loud bangs as police carried out the operation.
In Sheffield, neighbours spoke of seeing plain-clothed police and scores of officers in the area between Dun Street and Cornish Street.
Similar scenes were reported in Huddersfield, where a large number of armed police were deployed in the Ellison Street area of the town.
A spokesperson added: “The public may have heard loud bangs at the time that police entered the property. We would like to reassurance you that this was part of the method of entry to gain access to the property.
“We understand that people may have concerns as a result of this activity and we are grateful for the patience and understanding of the public while these enquiries are carried out.”