As jbtsax says, you have to tune your playing with your own ears. Use the tuner to set your sax up before you start playing then put it away while you play to your favourite song/backing track.
As a beginner, you're not going to be playing quick songs but still make an active choice to practise some slow ones/ballads specifically as a way to hone your intonation. The trick here is to balance the volume of the song with the volume of the sax so that you can hear yourself within the music as this makes hearing your intonation much, much easier. Backing tracks with a guide melody really come into their own for this as you're pitching your playing to a clear melody.
There are a number of reasons why I think this is a good excercise. First off, you're playing a song you like - that's always fun and far more likely to keep your interest than playing individual notes while staring at a tuner. Next, you're learning to play and listen at the same time, which is of paramount importance. That may sound odd at the moment but it should very quickly make sense. Also, I think this helps bring confidence to your playing because you'll really hear yourself improving because you've learned to listen while playing. You're not teaching yourself to play half-heartedly as you constantly try to change the pitch of your note to what the tuner says is in tune.
No one will ever be 100% perfect no matter how long they've played for or how much they practice - having a tuner constantly telling you you're out of tune is never going to acheive anything other than to destroy your confidence. I'm doing a lot of recording at the moment for various lockdown videos and I'm playing with other wind players who've got decades of experience and who sound incredible. Not one of them has produced a recording that was 100% in tune.
That's not to say tuners don't have a place, especially when it comes to problem solving certain issues, but at the moment learning to hear yourself playing while you're playing will be far more productive and positive.