I can't tell if the temperature change is good or bad. When you say a temperature deviates from the baseline that implies that the change is bad (maybe heating due to over current condition?). If the process and change is a good thing then use more positive words: exceed, surpass, or rise above all provide a positive view.
Example of describing a bad condition
If the temperature deviates from the baseline for more than 10
seconds then the over current alarm will activate.
A sentence like this will warn the user of the result of the temperature change. There is a negative feeling associated with "deviates".
Example of a good condition
After the temperature has exceeded the baseline for more than 10
seconds then the process will start.
You could use a sentence like this to describe a good result that the user is attempting to create.
Some notes on your original sentence
First time periods cannot be described as having a value. Time periods have a duration. Actions resulting from a trigger condition being met are best described as occurring instead of happening.
Ten seconds is the duration of the time period for which the temperature must deviate in order for Y to occur.
This sentence is most like your original goal, but does not sound natural and I cannot find a good context it would fit in. It is quite understandable though.
After the temperature has deviated for ten seconds Y will occur.
This sentence would best fit into a description of steps in a process.
If the temperature deviates from baseline for more than ten seconds Y will occur.
This sentence puts the emphasis on informing the operator of what will happen if the temperature changes.