He scored 71 not out as Pakistan survived a minor scare to chase a modest 198-run target in the first of two day-night games held here to raise funds for victims of last year's Kashmir earthquake.
Pakistan were strongly placed at 146-2 before losing two wickets in the space of three runs, but Younis batted steadily to ensure victory with nine balls to spare.
Skipper Inzamam-ul-Haq (40) and Mohammad Yousuf (one) fell in quick succession before Younis finished the match in the company of wicket-keeper Kamran Akmal (24 not out).
Younis, who put on 86 for the third wicket with Inzamam, struck one six and four boundaries in his responsible 24th half-century.
Pakistan, who lost the last four matches against India at home in February, ended their dismal run with a disciplined all-round peformance.
The match, also watched by Pakistan's President Pervez Musharraf, was the first to be held at the 16,000-capacity Zayad Cricket Stadium which became the second venue after Sharjah to host one-dayers in the United Arab Emirates.
Off-spinner Shoaib Malik also played a key role in his team's win, capturing three wickets to restrict India to a small total.
India, fresh from a recent 5-1 triumph against England at home, found runs hard to come by on a slow pitch where stroke-making was difficult.
Malik made batsmen struggle with his tidy line and length to finish with 3-40, including the wicket of in-form aggressive batsman Mahendra Dhoni (three).
Middle-order batsman Venugopal Rao top-scored for India with an unbeaten 61, his best in 14 one-day internationals. Even he was not allowed to score freely as he hit just three fours in his 93-ball knock.
Pakistan's fielders backed their bowlers remarkably well, bringing off four run-outs.
India's problems began when skipper Rahul Dravid (20) and Irfan Pathan (26) were caught short of the crease in quick succession. The innings also ended in a pair of run-outs, the victims being Harbhajan Singh and Shanthakumaran Sreesanth.
Rao gave a good account of himself on a difficult track, steadying the innings with a 64-run stand for the fifth wicket with teenager Suresh Raina (40) after his team had been reduced to 72-4.
Proceeds from Tuesday's match will be donated to the survivors of the massive earthquake that hit Kashmir last October killing more than 73,000 people in Pakistan and 1,300 in India.
Revenues from the second game on Wednesday will be shared by the Indian and Pakistan cricket boards after a million dollars is given to the hosts.
7-171, 8-180, 9-196
Fall of wickets: 1-42, 2-60, 3-146, 4-149
Result: Pakistan win by six wickets
Umpires: Rudi Koertzen (RSA) and Brian Jerling (RSA)
TV umpire: Tyron Wijewardena (SRI)
Match referee: Roshan Mahanama (SRI)