Well Yugi/Atem/Yami technically did lose fairly to Marik Ishtar/Dark Marik in the final duel of the battle city tournament. Atem did not win this duel, yami marik won this duel, odion saved atem from suffering.
Most people think marik was a weak duelist yet ignore the fact that he was praised by kaiba, atem and managed to defeat the main villain of the show (Bakura), he adapted to the new rules of the game in Battle City really easily. Atem/Yugi would not have been able to draw a card and clearly lost the duel, all Marik had to do was end his turn then atem would have decked out and lost.
Marik is the only canon loss that Atem suffered: https://yugioh.fandom.com/wiki/Yu-Gi-Oh!_-_Episode_142
Their are three more times where he lost a duel fairly but the problem with those incidents is that they are filler and thus not considered canon.
1) Raphael truely defeated Atem & Yugi in their first duel during the orichalcos arc. This has already been mentioned multiple times, even in their second duel raphael would have won if he didnt sacrifice all his life points to bring his monsters back that he did not use to duel anymore. His first duel with Atem was a clear victory where Atems lifepoints dropped to zero.
2) Gansley (the first member of the "big five") would have won his duel with Atem if it wasn't for the illogical plot, he literally had the opportunity to win but choose not to, he decided to drag things out instead.
Atem had low life points (only 500) and his monsters were in attack mode, he had nothing to defend himself and it was gansley's turn, while Gansley had two monsters he could tribute to summon a monster with 2200 atk points and celtic gaurdian only had 1400 he would have done 800 points of damage defeating Atem.
Source: duel monsters saga virtual world
3) Bakura (in episode 13) their first ever duel in duelist kingdom rules was anime only, yami bakura was literally winning the whole entire duel until the plot kicked into save the main character from losing and yami bakura switched bodies with regular bakura.
Source: Duel monsters episode 13
Atem was a lucky duelist who rarely won due to skill.