Don't meditate with a timer
I just had my longest, and also one of my best, seated meditations. The reason it was so lovely was that I finally gave up on using a timer. Instead, I started a stopwatch and left it.
I didn't realize how much the anticipation of the timer finishing was interrupting my meditation. One of the common sayings regarding meditation is that you shouldn't meditate toward a goal. Usually this means that you shouldn't be striving for "enlightenment." But even having the goal of sitting for 5 minutes is a distraction.
I can't tell you the best way to practice, but if you are struggling with a timed meditation session—start a stopwatch, hide it from sight, and see how long you can sit without the expectation of a timer going off.