According to a stock exchange announcement, Lloyds netted £344 million from the disposal, which represented 98 million shares at a price of 352.5p each.
The sale came at a 3.2% discount to the price SLA's shares closed at on Thursday night.
Relations between Lloyds and SLA have deteriorated since the bank's decision to pull a £109 billion mandate from the asset manager earlier this year.
Last month SLA said it disputed the decision and was locked in talks with Lloyds to find a resolution.
Lloyds inherited a 9.9% stake when Aberdeen bought its asset management business, Scottish Widows Investment Partnership, back in 2013.
The interest was diluted to 3.3% following last year's merger between Standard Life and Aberdeen.
Commenting on the disposal, Lloyds said: '[The holding] supported the partnership agreements that were previously in place with Standard Life Aberdeen but given notice has been served for these agreements, and we are not a natural long term holder of equities, we have now made the decision to sell the stake.'