He posted a six-under 66 at the weather-interrupted tournament, which has been reduced to 54 holes, to lead three-times Asian Tour winner Chapchai Nirat of Thailand, who signed for 67, by one stroke.
Filipino Antonio Lascuna is tied for third with India’s SSP Chowrasia, Australia’s Unho Park and Korean-American David Lipsky at the Asian Tour’s season-ending event.
“The multiple disruptions that were caused by the weather throughout the week made it a challenge for the tournament to be completed over 72 holes. As such, we have taken the decision to reduce the tournament to 54 holes,” said tournament director Wanchai Meechai
That means Sunday's third round will be the final one.
Chopra, who won the Johor Open in 1993 and just missed out to Joost Luiten last year, played his entire second round on Saturday, just finishing it as play was suspended at 1.45pm for three hours.
"I’m very lucky to be able to putt out on the last," he said. "I’ll get another afternoon off and watch it rain. It was almost similar on the first day where we were the last group to finish.
"I was on the good side of the draw this time but I’ve been on the bad side before. It all evens out but it is definitely an advantage."
Chapchai, who recently became a father, is looking to translate two top-10s into a win for the first time this season at the Asian Tour's final event.
“I want a good result for my newborn son, who we welcomed in our family last week. It doesn’t matter if I win or not but I want to play well for him," he said.
"It has been quite a while since I saw my name on top the leaderboard."
Marcus Fraser is on course to become the first Australian to win the Asian Tour Order of Merit after shooting a 68 to better Thailand’s Thaworn Wiratchant by two shots.
134 - Daniel CHOPRA (SWE) 68-66
135 - Chapchai NIRAT (THA) 68-67
136 - Antonio LASCUNA (PHI) 68-68, Unho PARK (AUS) 65-71, S.S.P. CHOWRASIA (IND) 67-69, David LIPSKY (USA) 63-73
137 - Scott BARR (AUS) 72-65, Thongchai JAIDEE (THA) 66-71, Sergio GARCIA (ESP) 68-69, Felipe AGUILAR (CHI) 67-70, Angelo QUE (PHI) 67-70, Shiv KAPUR (IND) 67-70