The pair, aged 18 and 20, were detained in the Albertbridge Road area on Saturday.
They were both charged with disorderly behaviour. The 20-year-old was also charged with provocative conduct.
They are due to appear at Belfast Magistrates' Court on Monday.
A 15-year-old boy who was arrested in the area has been released unconditionally.
Loyalists returned to the east of the city following a peaceful protest at Belfast City Hall on Saturday afternoon via the lower Newtownards Road near the Short Strand interface.
The Albertbridge Road and Castlereagh Street were closed while a flag protest took place.
The demonstration ended without the scenes of violence and rioting which broke out in the area after previous weekend flag protests.
Police said neighbourhood policing teams were involved in patrolling the interface on Saturday.
Earlier at City Hall, 600 people gathered to voice their opposition to a council decision to fly the Union flag on 18 designated days instead of 365 days a year.
They made their way to the city centre for the seventh week since the dispute began amid a heavy police presence.
Meanwhile a PSNI spokesperson said a protest also passed without incident in Carrickfergus, Co Antrim where a road block was cleared by police.
The Union flag is flying at Belfast City Hall on Sunday to celebrate the Countess of Wessex's birthday - one of the designated days.