Mas was banned from holding public office for two years in March 2017 for pushing ahead with the symbolic vote that was declared illegal by the courts.
His successor Carles Puigdemont staged another independence vote last year in the northeastern region.
The audit office — which oversees public spending — said Mas and nine members of his administration were responsible for the spending on the November 2014 referendum which amounted to 4.9 million euros.
The funds were used to create a website for the ballot, buy 7,000 computers used in voting centres set up in schools and other public buildings, print ballots and pay for advertising for the vote, the office said.
While the office ordered the ten to repay the money to state coffers “to the extent of their possibilities”, it cited Mas, who was Catalan leader from 2010 until 2016, as the main responsible party for the payment of the fine.
Around 80 percent of those who cast their ballot in the 2014 vote did so for independence — although just 2.3 million people out of a total of 6.3 million eligible voters took part.
Catalonia's parliament declared independence to no effect on October 27th last year following another banned secession referendum staged by Puigdemont's government. That triggered Spain's worst political crisis since the death of dictator General Francisco Franco in 1975.
The central government sacked the Catalan government, took control of the region and called a snap regional election.
In a separate case, Spain's Supreme Court last month ordered 18 former Catalan leaders to stand trial over last year's declaration of independence.
Prosecutors are seeking jail terms of up to 25 years on charges of rebellion or misuse of public funds over the failed secession bid. The sensitive trial is expected to start in early 2019.