Nestor, 41, will chase a fifth tournament title when he and Zimonjic, seeded fifth, play either Jesse Huta Galang of the Netherlands and Frenchman Stephane Robert or Italy's Fabio Fognini and Austrian Jurgen Melzer.
Nestor and Zimonjic needed just over an hour to win their semifinal event after last week losing in the semifinal round at Monte Carlo to Americans Bob and Mike Bryan, the world's top-ranked team.
Nestor won the Barcelona title in 2004 and 2006 with Mark Knowles and in 2009 and 2010 alongside Zimonjic. Dodig and Melo lost to Nestor and his partner in last year's quarter-finals.
Nestor and Zimonjic won the doubles title in Sydney in January before dropping the Dubai final a month later.
"We played a good match and it's great to get to the final," said Nestor, with the win giving his team a bye in the upcoming Madrid Masters. "We played well in the first set and got a lead in the second.
"We lost the game at 5-2 by getting a bit impatient but were able to creep back into it at the end."
Nestor and Zimonjic earned the opening set on a break in the fifth game and also broke Melo in the fifth game of the second set.
But leading 5-2, their play slipped somewhat, allowing their opponents to rally and save two match points along the way.
Nestor closed out match with consecutive aces in the final game.
"We've been playing well since the start on the clay, we might even have won some games with luck," Nestor said. "But we are on good form and playing solid.
"I think we've had those qualities in both of our weeks on the clay."