Get another envelope for "items purchased online." When you make a purchase online, pull out the equivalent amount of money from the proper envelope (household, gifts, entertainment, etc.) and put that money into the "items purchased online" envelope. (The amount grows as you purchase things, which is opposite of the other envelopes, which get spent down as you purchase things.)
Then, the next time you fund your envelopes, withdraw the difference of what you have in your "items purchased online" envelope, and then add that to what's in the "items purchased online" envelope, and fund your envelopes as you normally do.
Example: Let's say you buy $25 in DVDs from Amazon and $85 in clothing from Kohls.com. You'd take $25 out of your Entertainment envelope, and $85 from your Clothing envelope, and put that $110 in your "items purchased online" envelope. (The rest are cash purchases.) If you fund your envelopes with $500 each period, then you'd withdraw $390 ($500 - $110), empty the "online" envelope, and fund your envelopes as usual. Now your "online" envelope is zero again, and you rinse and repeat.