Spoilers here on episodes 7 and 8 of Attack on Titan (anime), and the 45th chapter of Attack on Titan (manga).
Towards the end of the battle between Eren and Reiner (Armored Titan) that occurred in episode 7 of Season 2 of Attack on Titan, we see Eren place Reiner in a special hold wherein Reiner's head is trapped within Eren's arms. Unable to break this hold, Reiner calls out to Bertolt (Colossal Titan) three separate times. At that point, Bertolt falls over and we later see that Eren is captured. Episode 8 of Season 2 provides some information as to why Eren lost his arms after this fight, but doesn't shed light on the actual events that led to Eren being captured.
If you reference back to the same place in the manga,
We find out that when Reiner called for Bertolt, the Colossal Titan's "plan" so-to-speak was to literally fall on top of both Eren and Reiner because only Reiner as the Armored Titan would be able to withstand the force of impact. The force of impact was so strong that the body of the Colossal Titan evaporated once he landed on the other two titans, and it blew a large gust of heat and wind pressure straight up the wall which prevented anyone from going down to help Eren. Since Reiner was the only titan capable of withstanding that impact, he was then able to pull Eren from from the nape of Eren's neck because the force of impact left Eren incapacitated.