Ms Harper, 50, of Crest Rd, Croydon, South London, stole £2,463,750 via 93 false invoices between December 2007 and December 2011.
This coincided with the period when the bank, which also owns Scottish Widows, Halifax and Bank of Scotland, was being bailed out with taxpayer money.
Ms Harper created a false bank account in the name of a software firm which carried out work for Lloyds. She had a personal friendship with the managing director of the software firm and personally advised him the problem was resolved when he questioned the invoices.
She had she could have been earning four times her £60,000 salary with her expertise at another bank but stayed with Lloyds out of loyalty to the bank.
She pleaded guilty to the charges of fraud by abuse of position and money laundering.
Defence counsel Carol Hawley said Ms Harper had been under a "huge amount of pressure" at the firm where she worked in two roles as senior manager for third party suppliers and interim head of fraud and security for digital banking.
She said: "She was not a greedy woman indulging herself in an extravagant lifestyle. Her personality causes her to feel she has to meet the needs of others."
She said Ms Harper had so far paid back £709,000 and expected to pay back more following the sale of her brother's house which she had helped to purchase.
At Southwark Crown Court, Judge Deborah Taylor told Ms Harper she had "abused her position and knowledge of the banking system" and "disregarded her duties out of a sense of entitlement."
She sentenced Ms Harper to five years for fraud and four for money laundering to be served concurrently. She will serve half before being released on licence.