Pilots at AirTran Airways and Southwest Airlines voted to approve a deal to combine their seniority lists, resolving a contentious issue and avoiding a setback that could have derailed the integration of the two carriers.

In voting that ran from Oct. 8 through Monday, 83.6 percent of the pilots that voted at each carrier cast ballots in favor of the deal. About 94 percent of the AirTran pilots and 95 percent of the Southwest pilots participated in the voting.

The deal will combine the roughly 1,700 AirTran pilots and 6,000 Southwest pilots onto a single seniority list and eventually bring significant pay increases to AirTran pilots.

AirTran pilots union leader Linden Hillman said in a written statement that the agreement "cements the bond between our two pilot groups, and helps clear the path to complete integration of the two carriers."

Dallas-based Southwest closed its acquisition of Orlando-based AirTran in May. AirTran's largest hub is in Atlanta and once integration is complete, the entire combined carrier will be known as Southwest.

Pilot seniority is a touchy issue in any airline merger, as it can determine their pay, work schedules and career prospects.

After a previous pilot seniority deal fell apart in August, a Southwest spokesman said if the company received a no vote on this deal, "it means that we cannot execute the original integration plan and we will have to reset." Southwest management was eager to see the new seniority deal approved to avoid going to arbitration.

The airline raised the possibility of a "Plan B" scenario, in which AirTran may not be fully integrated into Southwest as  planned -- which could put AirTran pilot jobs at risk. A presentation to AirTran pilots by their union leadership laid out the Plan B scenario.

But with the deal approved Monday, AirTran pilots will gradually transition to Southwest pay rates and positions, starting next April and to be completed by the end of 2014, according to union documents. The first deal had included an increase for AirTran pilots to Southwest pay rates next year.

But AirTran pilots will retain their longevity with AirTran after they move to Southwest and would not be furloughed before the transition is complete, "unless prohibitive conditions occur."