I just upgraded to El Capitan and was having the same issue. I've gotten used to swiping left or right with three fingers in a browser to go back or forward.
In trackpad settings, try unchecking the box next to "Swipe between pages." Close and reopen system preferences, then check the box and choose "Swipe with three fingers" from the list. That's what should fix it, theoretically.
What actually worked for me was enabling three finger dragging for the first time. System Preferences > Accessibility > Mouse & Trackpad > Trackpad Options > Enable Dragging > "three finger drag," click OK. I played around with this setting for a minute and then unchecked the "Enable Dragging" box. When I went back to System Preferences > Trackpad, I noticed that the box next to "Swipe between pages" was now unchecked. I checked it, selected "Swipe with three fingers" and I'm able to three-finger swipe back/forward in Chrome and Safari.
Hope this helps!