It is unknown when or where Tobias encountered Latios although it can be speculated that he used Darkrai to catch him because of Darkrai's type advantage. However this is unconfirmed and it is possible that Tobias might have caught Latios before Darkrai.
Latios was Tobias' second Pokémon during his battle with Ash, after Ash's Sceptile defeated Darkrai. Latios easily defeated Sceptile with Giga Impact, overpowering Leaf Blade and then battled Swellow. Swellow was unable to land a single blow on Latios and was defeated by a single Luster Purge. Ash then sent out Pikachu to battle the legendary Pokémon. At first Pikachu wasn't able to do much damage to Latios with the Eon Pokémon overwhelming Volt Tackle, Quick Attack and Iron Tail using Giga Impact, which due to Latios' greater size and weight, was able to overpower all three attacks. Realizing that raw power wasn't enough to defeat Latios, Ash changed tactic and had Pikachu jump onto the Eon Pokémon's back and hit it with several close range Thunderbolts. Latios used Light Screen and then threw Pikachu off and tried to finish it with its signature move Luster Purge. However Pikachu countered with a combination of Volt Tackle and Iron Tail which he used to charge straight into Latios' attack, resulted in a massive explosion which knocked out both Pokémon.