A Cameroon international, the 27-year-old midfield player underwent a medical on Friday and has agreed a deal until June 2014.
He will be eligible to play when he completes the formalities of securing a work permit, a process which could take up to two weeks.
"I am thrilled to be here at Aston Villa," Makoun said. "I am really, really happy and very proud to have joined a great club."
Makoun said Villa had been after him for a while, so he is delighted the deal finally happened. He can't wait to get started.
"I've left a very good club in Lyon, a side which has played Champions League football, but I am very excited by this new challenge at Aston Villa. Villa really want to do well and really want to achieve something, so I am really excited to be joining."
Aston Villa manager Gerard Houllier said, "Jean is a player who can play in front of the defence as a sitter and defensive midfielder or as a box-to-box midfielder. He has several assets about his game. He is also a very experienced player because he played Champions League football with Lille and Lyon.
"He is a nice guy too. I think he will settle well in the dressing room."
Houllier is delighted to get his man after previously attempting to sign him when manager of Lyon and the player was plying his trade at Lille.
Makoun began his career in his native Cameroon at Cotonsport Garoua, where he was part of the team's youth set-up.
Following this, he spent time at fellow Cameroonian sides Jeunesse Star and Tonnerre Yaounde, before eventually moving to France to join Ligue One side Lille.
Makoun became a firm fixture in the Lille side and a firm favourite, making more than 150 appearances in the country's top-flight and playing Champions League football too.
The 27-year-old opted to move to seven-time French champions Lyon in June 2008.
One of the highlights of his time with Lyon came in February 2010 when he scored the only goal in Lyon's first Champions League knockout round win over Real Madrid, hitting a looping shot from 25 yards out over the head of goalkeeper Iker Casillas.