The duration datatype is the correct type to represent this data, and you can plot durations.
In R2018a, there is a new capability to parse durations from text. It is limited to timer formats (e.g. hh:mm:ss) and right now doesn't support a comma as a decimal separator. However, if your data is coming from text, you can use ImportOptions to specify the decimal separator. Something like
opts = detectImportOptions(fi);
% if the first variable is your time data as strings
opts = setvartype(opts,1,'duration');
opts = setvaropts(opts,1,'DecimalSeparator',',')
t = readtable(fi, opts);
plot(t.Var1,t.Var2)
If you're using an earlier release, the best bet is to use datetime text parsing and then peel off the time-of-day part. This works unless you have durations that are longer than 24 hours.
d = timeofday(datetime("00:00:00,002",'InputFormat','HH:mm:ss,SSS'))
% show sub-second precision
d.Format = 'hh:mm:ss.SSS'
