The French club announced the capture on their official website on Tuesday, but did not disclose financial details of the deal.
However, French sport daily L'Equipe claim Lyon will have the option to sign Diakhate on a permanent contract for €8million (£6.6m) at the end of the season.
Senegal international Diakhate, who had been heavily linked with a move to Arsenal this summer, joined Dynamo three years ago from boyhood club Nancy but has been unable to hold down a regular spot in the first team.
The 26-year-old spent the second half of last season on loan at Lyon's Ligue 1 rivals St Etienne, helping the French side avoid relegation.
Diakhate's transfer deadline day capture sees him become Lyon's third major summer signing following the arrival of winger Jimmy Briand from Rennes and former Bordeaux playmaker Yoann Gourcuff.