The draw for the last eight of the Europa League took place on Friday, with both Premier League clubs drawn away from home first in their respective ties.
But with UEFA having confirmed that if both sides are drawn to play at home in the same week, Arsenal's legs have now been switched.
UEFA said the decision was made by local authorities, who do not want both London clubs to be playing in the city on the same day.
According to UEFA Club Competitions Committee principles, it is Arsenal's tie which has been altered in this situation due to Chelsea - who will take on Slavia Prague in the last eight - having higher priority after winning the FA Cup last season.
An explanatory statement released by UEFAbefore the draw read: “Following a decision made by the relevant local authorities, Chelsea FC and Arsenal FC cannot play at home on the same night.
“Should both clubs be drawn within the same sequence (home or away), the team having the lower priority – in this case Arsenal FC because Chelsea FC won the FA Cup - will be reversed in accordance with the UEFA Club Competitions Committee principles.
“The match schedule for the quarter-finals (including a potential reversal involving Arsenal FC) will be communicated to all parties at approximately 14.45 CET on Friday 15 March.
“The calendar for the semi-finals (including a potential reversal involving Arsenal FC, for the same reasons, if both clubs from London are still remaining in the competition) will be communicated to all parties on 20 April at the latest.”
Arsenal are not the only side facing potential scheduling issues in continental competition, with Premier League rivals Manchester United are in the same position.
The Red Devils have seen their own Champions League tie with Barcelona reversed, with the first leg now at Old Trafford.
That is because Man Utd finished behind City – who captured the title in record-breaking style – in the Premier League last season.