The EU legislative process has a direct-democratic tool called the European Citizens' Initiative. The tool is described in Article 11, Paragraph 4 of the Treaty on European Union and Article 24, paragraph 1 of the Treaty on the Functioning of the European Union.
However, this only proposes legislation to the EU commission which is then free to reject it.
The EU does currently not have a mechanism for binding EU-wide referendums.
However, there is plenty of precedent for national-level referendums in lots of countries which did not have a defined process for referendums either. This was usually implemented through an act which calls for one binding referendum on that one specific issue. So it would definitely be theoretically possible for the EU to hold a referendum on one specific issue by simply making a regulation which says it will only become effective after a referendum.
However, there is little motivation for the EU commission to do that.
A referendum is usually done when a state wants to do something they are sure the population wants but they can't do it because of political pressure (like the greek bailout referendum which was successfully used to reject the conditions dictated by the EU) or to solve an internal dispute (like the brexit referendum which was an unsuccessful gamble by Cameron to silence the EU critics within his party).
But the EU commission is quite unanimously pro-TTIP and seems determined to get the treaty finished as quickly and silently as possible. A referendum and public discussion would be counter-productive for their position. They have no reason to propose it as a referendum to the EU parliament when they can just as well do it without. Should the EU parliament reject the TTIP (although a year ago the parliament approved to keep negotiating), then a second attempt to propose it bound to a referendum might be a last ditch effort by the commission. But it is unlikely to be successful because they also know that large parts of the population have a negative opinion about TTIP by now. Also, the parliament could reject that proposal too. So it is unlikely that the commission will try that way.