The Afterburn effect, aka Excess Post-exercise Oxygen Consumption occurs regardless of the time of day the exercise happened. The main thing it depends on is the intensity of the exercise. So, whether you exercised in the morning or evening, your EPOC should be similar as long as the intensity applied is similar.
Are there benefits to exercising in the morning? Although that varies by individuals, on average, the answer is Yes!
According to this and this articles, exercising before breakfast results in more fat loss than later in the day.
Also, exercising in the morning reduces procrastination. When you workout in the evening, there's the tendency to skip because of many reasons: tiredness, laziness, emergencies, etc. An exercise missed is an exercise that cannot be recovered back. Working out in the morning reduces that possibility.
Morning exercises gives you an energy boost throughout the day, thus resulting in even higher calorie burn. If you've had the experience of exercising before work, you'll notice an increase in energy throughout the day (as long as you didn't exhaust yourself). Also, morning exercises allow you to increase your intensity (because your energy hasn't been used for other daily issues).
Caveat: Exercising in the morning, by itself, will not yield more benefits than in the evening. If the same intensity were applied, both morning and evening exercises should generate similar results. But when the related effects of morning exercises are added, it makes exercising in the morning a better option than in the evenings.