I have a longer post on this, including why you would want to clone using Thunderbolt and Disk Utility, but Apple decided to switch up Disk Utility's interface completely in El Capitan (10.11). Even though the process is similar, the exact steps are different.
One procedural difference worth noting: In Yosemite (10.10), Mavericks (10.9), etc., you would select the source, and then select what you wanted to restore the source to. In El Capitan (10.11) and supposedly beyond, you start by selecting the destination, and then select what source you want to restore from.
Open up Disk Utility (from /Applications/Utilities). Select the disk you want to restore to. And then select Edit > Restore.
You have the option to restore from another disk (if you have a computer connected via Thunderbolt, it should show up in the drop-down list) or to restore from a disk image (click Image... to find the image you want to restore from), and then click Restore.
Wait for it to restore.
Click Done when it's done restoring.