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49ers QB Colin Kaepernick got into a heated exchange with Oakland Raiders linebacker Sio Moore during halftime this weekend ... with Sio calling Colin a "bitch ass motherf**ker."

TMZ Sports has the footage ... showing Moore talking smack to 49ers players as they ran into the tunnel at halftime during Sunday's matchup.

Moore says something that grabs CK's attention and Kaepernick gets in his face -- saying, "I'm coming for you."

That's when you hear Moore fire back ... "Bitch ass mothef**ker."

As the two separate, 49ers defensive tackle Tony Jerod-Eddie steps in ... yelling, "I'll fire your ass up."

The Raiders came out and dominated the second half ... and won the game 24-13.