I have a chevy malibu automatic, it seems that while I am driving my car pauses like it is shifting gears. Could this be a misfiring piston or something else?
From this extremely limited description there are countless possibilities, including but not limited to a misfiring cylinder. Is the Check Engine Light lit?
Pistons don’t fire ?
I can't tell much from the information provided.
How about a little more information. How long has this been happening? DId it start up and get worse, or has it remained about the same?
What year Malibu and how many miles do you have on it.
When was the last time (miles and months) that the spark plugs and wires replaced? How about the air cleaner, and fuel filter?
Is there a CEL (Check Engine Light) on?
Has the transmission fluid ever been changed?
It just started a few weeks ago. I had the upper and lower manifold fixed about 2 years ago, also I had the fuel injector replaced last year.
This is a 2001 malibu with around 110,000 miles on it. I had the air filter and oil filter replaced during the last oil change which was in July. I get full synthetic and don’t put many miles on it. I don’t usually drive during the week, I take public transport and only use it to go up to 60 miles on the weekends.
I started noticing it when I would go from 35 mph to 40 and now I can feel it when I an going from 55 to 60+. There is no check engine light on or any of the other idiot lights. 
How long has it been since you changed the transmission fluid on it?
Your car may actually BE shifting gears at those speeds. I have a different make & model car, but mine shifts gears between 35&40 and again between 55&60.
never
well I have had the car for 5 years and this is the first time I have actually felt anything.