The rights group calls on states with influence over the parties involved in the conflict to press them to bring a halt to attacks on civilians.
It also urges them to stop selling or supplying arms and ammunition to these groups, "given compelling evidence that they have committed crimes against humanity, until they stop committing these crimes and perpetrators are fully and appropriately held to account."
Reports of abuses such as those alleged in the Human Rights Watch report have complicated international efforts to support the opposition to al-Assad's government.
In more than two years of conflict, the opposition has fragmented across a wide ideological and geographic spectrum, according to Barak Barfi, a research fellow at the New America Foundation. While some are nationalists are bent on liberating their country from a ruthless regime, others view the conflict as a springboard to a global jihad.
The main support for Syrian rebels has so far come from the Persian Gulf monarchies of Saudi Arabia and Qatar.
U.S. aid has been limited largely to nonlethal assistance such as communications gear and medical equipment.
In July, the Obama administration began supplying small arms and ammunition to the rebels.
But American officials have struggled with how to back opposition groups without providing weapons to those linked to Islamic militants, such as the al-Nusra Front, a group considered the most effective anti-Assad force on the battlefield, but one the United States says has ties to al-Qaida.
Meanwhile, fighters from the Lebanon-based Shiite militant group Hezbollah are helping Syrian government forces.
A video posted to YouTube this week that purports to show Hezbollah fighters killing injured Syrians has angered many in the region. Hezbollah has not responded to the furor. It is not clear who the alleged victims are.