Unseeded Bopanna and Qureshi finally won an ATP doubles title together in their third attempt, having finished runners-up in both the previous final appearances -- in Mumbai (2007) and at Newport (2008).
The Indo-Pak duo had a dream run last year, winning three ATP Challenger events together, but were not able to clinch a Tour event.
For Bopanna, though, this is his second ATP doubles title after the LA Open triumph in 2008 partnering American Eric Butorac.
An elated Bopanna said, "Both of us are thrilled to have won this tournament. We had a great 2009 together, winning three ATP Challenger events, but were not able to clinch a Tour event. It's great to have begun this year on such a positive note by winning our first ATP World Tour trophy and we hope this is the first of many."
"I think it's a great achievement," Qureshi said.
"As a team we are really good and we can be in the top 10 definitely together. Today's win definitely proves it because the chips were really down and we were able to find the solution to get back."
It was Beck and Levy who had the momentum when the rain struck with the Slovakian-Israeli duo leading 6-2, 1-1 in the second set.
When play resumed, Bopanna and Qureshi broke serve in the sixth game to lead 4-2 before the later serving out the set to level the match.
In the deciding match tie-break, Bopanna and Qureshi played out of their skin to take it 10-5 and seal victory after 68 minutes.
"We started off a little tentatively. Obviously it was our third final together, which meant there was a little bit of tentativeness starting off," admitted Bopanna.
"The rain delay helped. We spoke a little bit. We said 'we're here to fight and win'. We came out and started winning by playing aggressive tennis, the way we do normally."
Bopanna and Qureshi, who had defeated second seeded Johan Brunstrom and Jean-Julien Rojer and third seeded Eric Butorac and Rajeev Ram in the last eight round and semifinal matches, will pocket 250 ranking points and share USD 24,350 in prize money for winning the SA Open.