In the groundbreaking agreement the union and the agency will agree national terms and conditions for third-party lecturers, staff development and promotion of each other's services.
Gerald Imison, the union's deputy general secretary, said: "We are concerned that agency lecturers in colleges have the same employment protection and benefits as their full-time permanent colleagues. The agreement ensures that there is direct trade union representation in this sector."
The deal comes a month after the TUC called such practices "shoddy" and amid concern over the role of ELS, who provide lecturers to around a third of colleges.
The TUC's Temporary Workers, Permanent Rights report, published last month concludes: "We would hope that there will be no repeats of the kind of changes that have occurred in colleges which have simply been a short-term money-saving operation I such shoddy employment arrangements will neither attract nor retain quality lecturers."
It emerged this week that the company may escape investigation under the terms of the Department for Trade and Industry report into agencies after the DTI wrote to ELS saying they were a "service provider" and not an agency.
A survey by the ATL's rival union, NATFHE, found widespread discontent among those employed by ELS. David Lott, the union's national officer, said: "Not a single respondent was happy with their general treatment or development opportunities.
"Not a single agency lecturer rated their working experience above average, with the majority describing it as poor or very poor."