The French publication reports that Levy was willing to table a £40.3m bid for the French playmaker, but the London club did not make a move in the end. Tottenham did not sign a single player this summer.
L'Equipe adds that another unnamed Premier League club did bid £44.8m for the 21-year-old Frenchman, but the bid was rejected by Lyon.
Ndombele made his professional debut at Amiens, making 39 appearances for the club as they secured promotion from the French second division.
Ndombele, who is of Congolese descent, spent last season on a season-long loan with Ligue 1 side Lyon last season - who paid Amiens a €2m loan fee - and made 54 appearances in all competitions.
Tottenham interested in Lyon's Tanguy Ndombele but no contact between clubs and Lyon do not want to sell the 21-year-old France U21 this summer.— Spurs Centre (@Spurs_Centre) June 19, 2018
Lyon made the signing permanent this summer, and fended off interest from a number of European clubs to keep the exciting young prospect at the Stade de Lyon.
The midfield playmaker scored twice during his time at Lyon last season.
Since making his debut for them in 2017, Ndombele has made nine appearances for the France Under-21 national team, becoming a key part of the Les Bleus midfield.
It will remain to be seen whether Tottenham return for the Lyon man in either the January transfer window or next summer, but with Spurs chairman Daniel Levy reportedly a fan of the up-and-coming midfielder there is a good chance of such a move in the future for Ndombele.