The commission last week issued a report stating that Davidson twice broke electoral law by missing the 30-day deadline for registering two donations totalling £14,500 in October.
The Glasgow MSP was fined £400, with each offence punished by a fixed penalty of £200. Davidson paid the fine on May 11.
Wendy Alexander, the former Scottish Labour leader who resigned in 2008 after accepting an illegal donation, was only forced to forfeit it, and was not fined.
Although fixed penalties are used for "isolated cases of lower-level non-compliance", the fine is still embarrassing for Davidson, as it will raise questions about her experience and competence.
A senior Tory source said: "This is just not what the party needs. It's the latest in a long set of embarrassing moments for Ruth."
Davidson, 33, a former BBC broadcaster, became Tory leader in November following a bitter and divisive contest triggered by the resignation of Annabel Goldie in May 2011. She was made leader just six months after becoming an MSP for the first time.
Despite being the favourite of the Tory hierarchy, she failed to secure the support of association chairs in her Glasgow seat, and her campaign was dogged by a series of self-inflicted errors.
In the closing days of the campaign, the three other Tory MSPs vying for the job accused her of receiving an unfair advantage through covert backing from Conservative HQ.
After a fleeting honeymoon period, Davidson has been the subject of mounting criticism from the Scottish Tories, with a surge in complaints after the party lost 20% of its vote and its councillors in May's local elections.
Last week, Alex Salmond taunted her at First Minister's Questions by reading out critical comments from Toryhoose – a Scottish Conservatives website – which had previously acted as Davidson's cheerleader, about the party's poor showing in the election.
The latest setback concerns money given to Davidson's leadership campaign last autumn.
Electoral Commission records show Davidson accepted £29,500 in four lots in her capacity as a "regulated donee", the term used when an individual MP or MSP accepts a donation.
Two donations were accepted on September 19 – a sum of £2000 from James Stewart, director of a private equity company who has also in the past given money to Scottish Tory MP David Mundell; and £12,500 from Glasgow-based property company Alchemist Estates Limited, owned by Conservative donor Brian Gillies.
By law, these should have been declared to the Commission by October 18, but Davidson failed to register them until November 21, when she also declared a further £10,000 from Stewart and £5000 from London-based donor Carolyn Ward.
In its enforcement report, the Commission said it had fined Davidson for "failure to deliver two donation reports within 30 days of acceptance of donations".
Davidson's main rival for the Tory leadership, Murdo Fraser, reported all of his donations on time.
SNP deputy leader Nicola Sturgeon: "This is a humiliation for Ruth Davidson and another blow for her flagging leadership."
A Labour spokesman said: "These rules are in place for good reason to ensure fairness and transparency in elections and it is appropriate this action is taken against Ruth Davidson."
John Lamont, Davidson's campaign manager, said: "Ruth referred the donations to the Electoral Commission as soon as the error was realised and assisted them at all points in the process."