A 23-year-old and a 27-year-old are in police custody after the raids in the early hours of the morning.
The arrests were made in Paisley and Dalmarnock in the east end of Glasgow. Both men have been charged with sectarian breach of the peace
Cops are hunting 50 people involved in incitement to attack the Lurgan man.
Supt Kirk Kinnell, from Strathclyde Police’s anti-violence directorate, said: “I would like to deliver a clear message to those who continue to make hate-filled comments and cause distress to decent members of the public, that we will pursue you relentlessly until this behaviour is stopped.
“Some people seem to think that they are anonymous online or can hide in a crowd, but technology can also be used to bring the police directly to you wherever you are.”
The raids, which police said were ongoing, target postings of religious and racial hate comments about Celtic manager Neil Lennon and Rangers striker El Hadji-Diouf.
An extra 1,000 officers will be out in Glasgow on Sunday for Celtic and Rangers last game of the season.
Lennon has endured sectarian threats against him throughout his career as a player and manager at Celtic and was the target of a parcel bomb campaign, which also saw devices sent to QC Paul McBride and MSP Trish Godman.
Mr McBride told the BBC: “The internet appears to be a driver for individuals to come together and spew their hatred and bile out.
“And I’m afraid it’s resulted in people dying. People are being stabbed in a sectarian way in Glasgow. As a person who works in the High Court as a QC every day of the week, I see the result of sectarian crime.”
First Minister Alex Salmond said there should be “no hiding place” for those responsible for sectarian abuse on the internet.
He said: “We also have to have key legal changes which make convictions in that area, because of corroboration, more possible, but we have already done that for different types of offences, for example sex crimes through the internet.
“It can certainly be done for sectarian crime.”