Use min/max and padding.

If you use min/max padding is ignored thus to have padding increase min/max.

by maccaroo

HTML

<script src="https://cdnjs.cloudflare.com/ajax/libs/jqPlot/1.0.8/jquery.jqplot.min.js"></script>
<div id="chart1" class="chart">

</div>
<div id="chart2" class="chart"></div>
<input id="button" type="button" value="click" />

CSS

.chart {
  height: 300px;
  width: 300px;
}

//jquery.jqplot.css

/*rules for the plot target div.  These will be cascaded down to all plot elements according to css rules*/

.jqplot-target {
  position: relative;
  color: #666666;
  font-family: "Trebuchet MS", Arial, Helvetica, sans-serif;
  font-size: 1em;
  /*    height: 300px;
    width: 400px;*/
}


/*rules applied to all axes*/

.jqplot-axis {
  font-size: 0.75em;
}

.jqplot-xaxis {
  margin-top: 10px;
}

.jqplot-x2axis {
  margin-bottom: 10px;
}

.jqplot-yaxis {
  margin-right: 10px;
}

.jqplot-y2axis,
.jqplot-y3axis,
.jqplot-y4axis,
.jqplot-y5axis,
.jqplot-y6axis,
.jqplot-y7axis,
.jqplot-y8axis,
.jqplot-y9axis,
.jqplot-yMidAxis {
  margin-left: 10px;
  margin-right: 10px;
}


/*rules applied to all axis tick divs*/

.jqplot-axis-tick,
.jqplot-xaxis-tick,
.jqplot-yaxis-tick,
.jqplot-x2axis-tick,
.jqplot-y2axis-tick,
.jqplot-y3axis-tick,
.jqplot-y4axis-tick,
.jqplot-y5axis-tick,
.jqplot-y6axis-tick,
.jqplot-y7axis-tick,
.jqplot-y8axis-tick,
.jqplot-y9axis-tick,
.jqplot-yMidAxis-tick {
  position: absolute;
  white-space: pre;
}

.jqplot-xaxis-tick {
  top: 0px;
  /* initial position untill tick is drawn in proper place */
  left: 15px;
  /*    padding-top: 10px;*/
  vertical-align: top;
}

.jqplot-x2axis-tick {
  bottom: 0px;
  /* initial position untill tick is drawn in proper place */
  left: 15px;
  /*    padding-bottom: 10px;*/
  vertical-align: bottom;
}

.jqplot-yaxis-tick {
  right: 0px;
  /* initial position untill tick is drawn in proper place */
  top: 15px;
  /*    padding-right: 10px;*/
  text-align: right;
}

.jqplot-yaxis-tick.jqplot-breakTick {
  right: -20px;
  margin-right: 0px;
  padding: 1px 5px 1px 5px;
  /*    background-color: white;*/
  z-index: 2;
  font-size: 1.5em;
}

.jqplot-y2axis-tick,
.jqplot-y3axis-tick,
.jqplot-y4axis-tick,
.jqplot-y5axis-tick,
.jqplot-y6axis-tick,
.jqplot-y7axis-tick,
.jqplot-y8axis-tick,
.jqplot-y9axis-tick {
  left: 0px;
  /* initial position untill tick...

JavaScript

$(document).ready(function() {
  function minMax(data) {
    var min = data[0];
    var max = data[0];
    for (var i = 1; i < data.length; i++) {
      var val = data[i];
      if (val > max)
        max = val;
      else if (val < min)
        min = val;
    }
    return {
      'min': min,
      'max': max
    };
  }
  var pad = 10;
  var data = [3, 7, 9, 1, 4, 6, 8, 2, 5];
  var test = minMax(data);
  console.log("min: " + test.min + "  max: " + test.max);
  //with min/max increased to move points away from the plot's borders
  $.jqplot('chart1', [data], {
    axes: {
      yaxis: {
				pad: 0,
        numberTicks: 5,
        tickOptions: {
          formatString: '%i'
        }
      },
      xaxis: {
      	pad: 0
      }
    }
  });
});