Rajoy accused Convergence and Union (CiU) of playing “petty politics” with their decision.
Generalitat President Artur Mas and Democratic Union leader Josep Antoni Duran confirmed their coalition's abstention when they met on Wednesday to discuss what King Juan Carlos’s abdication would mean for Catalonia.
They concluded CiU was right to abstain from the parliamentary vote which will see Crown Prince Felipe become king, but still wished the future monarch “all the wise choices and successes” possible during his reign.
Catalan President Artur Mas was most likely alluding to the November 9th consultation on independence he has been trying to persuade Madrid to approve.
In April, the Spanish Parliament deemed the vote illegal and said it wouldn't take place but Mas has vowed the vote will go ahead.
"In the end, the central government must abandon its political short-sightedness and leave Catalonia alone to hold the consultation," Mas told international news agency Reuters.
"This is a time in Catalonia when we have to unite in a joint effort, do things in a new way. When we are divided, in Madrid they are toasting us with champagne," he added.